Published in Methods Mol Biol on January 01, 2008
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
Long noncoding RNAs: past, present, and future. Genetics (2013) 3.16
Direct conversion of fibroblasts to neurons by reprogramming PTB-regulated microRNA circuits. Cell (2013) 2.43
SHAPE-directed RNA secondary structure prediction. Methods (2010) 2.40
Widespread genetic switches and toxicity resistance proteins for fluoride. Science (2011) 2.39
Retracted Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol (2010) 2.39
5'-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res (2012) 2.36
An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science (2010) 2.33
Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol (2010) 2.24
Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry (2011) 1.62
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res (2012) 1.58
Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX. Chem Biol (2012) 1.54
Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol (2009) 1.50
5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res (2010) 1.49
Challenges and opportunities for small molecule aptamer development. J Nucleic Acids (2012) 1.48
Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat Chem Biol (2013) 1.47
Regulation of transcription by long noncoding RNAs. Annu Rev Genet (2014) 1.43
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature (2009) 1.43
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res (2011) 1.32
Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol (2011) 1.29
Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol Mol Biol Rev (2015) 1.26
Sharing and archiving nucleic acid structure mapping data. RNA (2011) 1.20
Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Mol Cell (2016) 1.17
Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. Genes Dev (2012) 1.16
Challenges of ligand identification for riboswitch candidates. RNA Biol (2011) 1.16
A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem Biol (2010) 1.14
Exploring mRNA 3'-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Nucleic Acids Res (2013) 1.07
Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. Biochemistry (2010) 1.07
Structure and mechanism of purine-binding riboswitches. Q Rev Biophys (2012) 1.06
RNA as a boiling-resistant anionic polymer material to build robust structures with defined shape and stoichiometry. ACS Nano (2014) 1.05
Evidence for widespread gene control function by the ydaO riboswitch candidate. J Bacteriol (2010) 1.05
Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch. RNA (2010) 1.04
Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria. Biochemistry (2017) 1.03
Correlating SHAPE signatures with three-dimensional RNA structures. RNA (2011) 1.03
GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP. Proc Natl Acad Sci U S A (2015) 1.02
Importance of the NCp7-like domain in the recognition of pre-let-7g by the pluripotency factor Lin28. Nucleic Acids Res (2011) 1.00
Secondary structure is required for 3' splice site recognition in yeast. Nucleic Acids Res (2011) 0.98
Standardization of RNA chemical mapping experiments. Biochemistry (2014) 0.98
Antagonistic functions between the RNA chaperone Hfq and an sRNA regulate sensitivity to the antibiotic colicin. EMBO J (2013) 0.98
Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria. Biochemistry (2017) 0.97
The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis. Nat Chem Biol (2012) 0.96
Bacterial aptamers that selectively bind glutamine. RNA Biol (2011) 0.95
Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7). RNA (2013) 0.95
Structural effects of linkage disequilibrium on the transcriptome. RNA (2011) 0.95
An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches. RNA (2012) 0.95
The centrality of RNA for engineering gene expression. Biotechnol J (2013) 0.94
Mechanism for gene control by a natural allosteric group I ribozyme. RNA (2011) 0.93
Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes. Chem Biol (2014) 0.93
Synthesis and stereospecificity of 4,5-disubstituted oxazolidinone ligands binding to T-box riboswitch RNA. J Med Chem (2011) 0.92
A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori. Proc Natl Acad Sci U S A (2014) 0.92
Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A. J Mol Biol (2010) 0.92
Microfluidic screening of electrophoretic mobility shifts elucidates riboswitch binding function. J Am Chem Soc (2013) 0.91
The mutate-and-map protocol for inferring base pairs in structured RNA. Methods Mol Biol (2014) 0.90
A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis. Nucleic Acids Res (2012) 0.89
Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops. RNA (2010) 0.88
Control of bacterial exoelectrogenesis by c-AMP-GMP. Proc Natl Acad Sci U S A (2015) 0.87
Tandem attenuators control expression of the Salmonella mgtCBR virulence operon. Mol Microbiol (2012) 0.87
Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Mol Cell (2015) 0.85
Progress and challenges for chemical probing of RNA structure inside living cells. Nat Chem Biol (2015) 0.85
Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob Agents Chemother (2015) 0.84
Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling. Biochemistry (2014) 0.83
Small RNA modules confer different stabilities and interact differently with multiple targets. PLoS One (2013) 0.83
Impact of nuclear organization and dynamics on epigenetic regulation in the central nervous system: implications for neurological disease states. Ann N Y Acad Sci (2010) 0.82
Tackling structures of long noncoding RNAs. Int J Mol Sci (2013) 0.82
The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations. J Mol Biol (2013) 0.82
Two glycine riboswitches activate the glycine cleavage system essential for glycine detoxification in Streptomyces griseus. J Bacteriol (2014) 0.81
Mg(2+)-induced conformational changes in the btuB riboswitch from E. coli. RNA (2013) 0.80
Direct structural analysis of modified RNA by fluorescent in-line probing. Nucleic Acids Res (2011) 0.79
Selective inhibition of miR-21 by phage display screened peptide. Nucleic Acids Res (2015) 0.79
Structure-guided design of fluorescent S-adenosylmethionine analogs for a high-throughput screen to target SAM-I riboswitch RNAs. Chem Biol (2014) 0.79
DNA-rescuable allosteric inhibition of aptamer II ligand affinity by aptamer I element in the shortened Vibrio cholerae glycine riboswitch. J Biochem (2014) 0.79
Discovery and validation of novel and distinct RNA regulators for ribosomal protein S15 in diverse bacterial phyla. BMC Genomics (2014) 0.79
Non-nearest-neighbor dependence of stability for group III RNA single nucleotide bulge loops. RNA (2014) 0.79
An RNA aptamer specific to Hsp70-ATP conformation inhibits its ATPase activity independent of Hsp40. Nucleic Acid Ther (2015) 0.78
Data-directed RNA secondary structure prediction using probabilistic modeling. RNA (2016) 0.78
Riboswitch structure and dynamics by smFRET microscopy. Methods Enzymol (2014) 0.78
Transcriptional and posttranscriptional events control copper-responsive expression of a Rhodobacter capsulatus multicopper oxidase. J Bacteriol (2012) 0.78
Small antisense oligonucleotides against G-quadruplexes: specific mRNA translational switches. Nucleic Acids Res (2014) 0.78
Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine. J Mol Biol (2012) 0.78
Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol (2015) 0.78
Opportunities in the design and application of RNA for gene expression control. Nucleic Acids Res (2016) 0.78
Identification of ligand analogues that control c-di-GMP riboswitches. ACS Chem Biol (2012) 0.78
Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana. Biol Direct (2010) 0.78
The Bacterial Transcription Termination Factor Rho Coordinates Mg(2+) Homeostasis with Translational Signals. J Mol Biol (2015) 0.78
Biochemical analysis of the complex between the tetrameric export adapter protein Rec of HERV-K/HML-2 and the responsive RNA element RcRE pck30. J Virol (2012) 0.77
Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins. Nucleic Acids Res (2016) 0.76
A minimalist biosensor: Quantitation of cyclic di-GMP using the conformational change of a riboswitch aptamer. RNA Biol (2015) 0.76
Co-evolution of Bacterial Ribosomal Protein S15 with Diverse mRNA Regulatory Structures. PLoS Genet (2015) 0.76
Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. J Mol Biol (2016) 0.75
The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA (2016) 0.75
Identification of Spermidine Binding Site in T-box Riboswitch Antiterminator RNA. Chem Biol Drug Des (2015) 0.75
Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator. Nucleic Acids Res (2016) 0.75
Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res (2017) 0.75
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. RNA (2017) 0.75
Morpholino oligonucleotides do not participate perfectly in standard Watson-Crick complexes with RNA. RNA (2010) 0.75
Optimizing RNA structures by sequence extensions using RNAcop. Nucleic Acids Res (2015) 0.75
Tb(3+)-Cleavage Assays Reveal Specific Mg(2+) Binding Sites Necessary to Pre-fold the btuB Riboswitch for AdoCbl Binding. Front Chem (2017) 0.75
Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proc Natl Acad Sci U S A (2017) 0.75
RNA regulators responding to ribosomal protein S15 are frequent in sequence space. Nucleic Acids Res (2016) 0.75
Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem (2016) 0.75
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature (2002) 8.14
Gene regulation by riboswitches. Nat Rev Mol Cell Biol (2004) 7.00
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell (2003) 6.21
Control of gene expression by a natural metabolite-responsive ribozyme. Nature (2004) 6.04
Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol (2005) 5.66
Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol (2004) 5.44
An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci U S A (2002) 5.02
A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science (2004) 4.91
Genetic control by a metabolite binding mRNA. Chem Biol (2002) 4.85
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A (2004) 4.35
The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem (2009) 4.20
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature (2006) 3.90
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature (2007) 3.87
Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol (2003) 3.84
Riboswitches as versatile gene control elements. Curr Opin Struct Biol (2005) 3.83
The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol (2007) 3.80
An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol (2003) 3.75
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell (2005) 3.62
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res (2007) 3.59
Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA (2003) 3.42
An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev (2003) 3.37
Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol (2009) 3.28
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
Riboswitches as antibacterial drug targets. Nat Biotechnol (2006) 3.01
The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry (2005) 2.98
Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol (2006) 2.94
Tandem riboswitch architectures exhibit complex gene control functions. Science (2006) 2.63
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat Struct Mol Biol (2007) 2.52
Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res (2004) 2.47
Genetic control by metabolite-binding riboswitches. Chembiochem (2003) 2.32
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol (2005) 2.32
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA (2005) 2.28
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat Biotechnol (2005) 2.22
Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell (2007) 2.18
Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem Biol (2005) 2.00
Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA (2007) 1.96
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA (2006) 1.81
Ribozyme speed limits. RNA (2003) 1.68
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. RNA (2008) 1.67
Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environ Microbiol (2009) 1.61
R2R--software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics (2011) 1.60
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Proc Natl Acad Sci U S A (2007) 1.54
Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol (2009) 1.50
Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat Chem Biol (2013) 1.47
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature (2009) 1.43
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA (2008) 1.39
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell (2008) 1.38
Characteristics of ligand recognition by a glmS self-cleaving ribozyme. Angew Chem Int Ed Engl (2006) 1.38
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem Cell Biol (2008) 1.35
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol Microbiol (2008) 1.33
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA (2009) 1.32
Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chem Biol (2009) 1.29
Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol (2011) 1.29
Purine sensing by riboswitches. Biol Cell (2008) 1.24
Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins. Proc Natl Acad Sci U S A (2013) 1.22
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. BMC Genomics (2009) 1.21
Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiol (2009) 1.16
Finding non-coding RNAs through genome-scale clustering. J Bioinform Comput Biol (2009) 1.16
Challenges of ligand identification for riboswitch candidates. RNA Biol (2011) 1.16
A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem Biol (2010) 1.14
Integron attI1 sites, not riboswitches, associate with antibiotic resistance genes. Cell (2013) 1.10
Identification of a large noncoding RNA in extremophilic eubacteria. Proc Natl Acad Sci U S A (2006) 1.08
Molecular-recognition characteristics of SAM-binding riboswitches. Angew Chem Int Ed Engl (2006) 1.06
Evidence for widespread gene control function by the ydaO riboswitch candidate. J Bacteriol (2010) 1.05
Ligating DNA with DNA. J Am Chem Soc (2004) 1.01
Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res (2005) 1.01
An expanded collection and refined consensus model of glmS ribozymes. RNA (2011) 1.00
Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing. Nucleic Acids Res (2013) 0.97
Bacterial aptamers that selectively bind glutamine. RNA Biol (2011) 0.95
Substrate specificity and reaction kinetics of an X-motif ribozyme. RNA (2003) 0.94
Association of OLE RNA with bacterial membranes via an RNA-protein interaction. Mol Microbiol (2010) 0.94
Mechanism for gene control by a natural allosteric group I ribozyme. RNA (2011) 0.93
Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection. Nucleic Acids Res (2006) 0.92
Engineering high-speed allosteric hammerhead ribozymes. Biol Chem (2007) 0.92
Fluoride enhances the activity of fungicides that destabilize cell membranes. Bioorg Med Chem Lett (2012) 0.91
A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nat Struct Mol Biol (2009) 0.89
Small, highly active DNAs that hydrolyze DNA. J Am Chem Soc (2013) 0.89
Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate. Anal Chem (2012) 0.88
In vitro selection and characterization of cellulose-binding DNA aptamers. Nucleic Acids Res (2007) 0.86
Selection in vitro of allosteric ribozymes. Methods Mol Biol (2004) 0.82
The power of riboswitches. Sci Am (2007) 0.80
Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products. Biotechniques (2013) 0.80
Identification of ligand analogues that control c-di-GMP riboswitches. ACS Chem Biol (2012) 0.78
Mechanism and distribution of glmS ribozymes. Methods Mol Biol (2012) 0.77
Ancient, giant riboswitches at atomic resolution. Nat Struct Mol Biol (2012) 0.77
In vitro selection of glmS ribozymes. Methods Mol Biol (2009) 0.75
OLE RNA protects extremophilic bacteria from alcohol toxicity. Nucleic Acids Res (2012) 0.75
In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP. Methods Mol Biol (2014) 0.75