Published in Annu Rev Biophys on January 01, 2008
Regulatory RNAs in bacteria. Cell (2009) 9.57
The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem (2009) 4.20
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
Conformational selection or induced fit: a flux description of reaction mechanism. Proc Natl Acad Sci U S A (2009) 3.03
Prospects for riboswitch discovery and analysis. Mol Cell (2011) 2.84
TonB-dependent transporters: regulation, structure, and function. Annu Rev Microbiol (2010) 2.72
Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev (2010) 2.16
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput (2011) 2.12
Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure (2010) 2.02
Bacterial RNA thermometers: molecular zippers and switches. Nat Rev Microbiol (2012) 1.99
Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure (2009) 1.84
Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol (2011) 1.75
Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol Cell (2010) 1.66
Termination and antitermination: RNA polymerase runs a stop sign. Nat Rev Microbiol (2011) 1.59
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA (2010) 1.58
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet (2010) 1.56
Expanding roles for metabolite-sensing regulatory RNAs. Curr Opin Microbiol (2009) 1.55
Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX. Chem Biol (2012) 1.54
Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. Biophys J (2009) 1.51
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA (2009) 1.48
Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annu Rev Biophys (2012) 1.47
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature (2009) 1.43
Folding of a transcriptionally acting preQ1 riboswitch. Proc Natl Acad Sci U S A (2010) 1.34
Riboswitch RNAs: regulation of gene expression by direct monitoring of a physiological signal. RNA Biol (2010) 1.33
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res (2011) 1.32
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA (2009) 1.32
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics (2013) 1.32
Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution. Nucleic Acids Res (2010) 1.30
Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chem Biol (2009) 1.29
A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta (2009) 1.29
Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell (2012) 1.29
Computational approaches to RNA structure prediction, analysis, and design. Curr Opin Struct Biol (2011) 1.28
mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol (2010) 1.28
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold. RNA (2009) 1.26
Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature (2012) 1.26
Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus. Proc Natl Acad Sci U S A (2010) 1.23
Cooperative tertiary interaction network guides RNA folding. Cell (2012) 1.21
A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol (2010) 1.18
Riboswitch function: flipping the switch or tuning the dimmer? RNA Biol (2010) 1.18
Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc (2012) 1.18
Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiol (2009) 1.16
SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch. J Mol Biol (2010) 1.15
Comparison of solution and crystal structures of preQ1 riboswitch reveals calcium-induced changes in conformation and dynamics. J Am Chem Soc (2011) 1.13
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res (2009) 1.13
Amino acid recognition and gene regulation by riboswitches. Biochim Biophys Acta (2009) 1.11
Single-molecule correlated chemical probing of RNA. Proc Natl Acad Sci U S A (2014) 1.10
Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding. ACS Chem Biol (2012) 1.09
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Nat Chem Biol (2014) 1.07
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry (2011) 1.07
Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. Proc Natl Acad Sci U S A (2012) 1.07
Differential analogue binding by two classes of c-di-GMP riboswitches. J Am Chem Soc (2011) 1.07
Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. Biochemistry (2010) 1.07
Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi. Nucleic Acids Res (2010) 1.06
Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease. J Am Chem Soc (2010) 1.06
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res (2011) 1.06
Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng (2011) 1.05
Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. J Mol Biol (2009) 1.04
Recognition of S-adenosylmethionine by riboswitches. Wiley Interdiscip Rev RNA (2011) 1.03
Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy. Nucleic Acids Res (2011) 1.03
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm. Nucleic Acids Res (2009) 1.02
The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. Nat Struct Mol Biol (2011) 1.02
Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç. Nucleic Acids Res (2009) 1.01
Design principles for ligand-sensing, conformation-switching ribozymes. PLoS Comput Biol (2009) 1.00
In vitro selection of structure-switching, self-reporting aptamers. Proc Natl Acad Sci U S A (2010) 0.99
Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch. Nat Chem Biol (2011) 0.99
Structure and function of the T-loop structural motif in noncoding RNAs. Wiley Interdiscip Rev RNA (2013) 0.99
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J Am Chem Soc (2012) 0.98
Clustering to identify RNA conformations constrained by secondary structure. Proc Natl Acad Sci U S A (2011) 0.98
Structural determinants for ligand capture by a class II preQ1 riboswitch. Proc Natl Acad Sci U S A (2014) 0.98
The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis. Nat Chem Biol (2012) 0.96
Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition. RNA (2009) 0.96
Probing the dynamics of the P1 helix within the Tetrahymena group I intron. J Am Chem Soc (2009) 0.94
Multiple metal-binding cores are required for metalloregulation by M-box riboswitch RNAs. J Mol Biol (2009) 0.94
Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics. J Am Chem Soc (2009) 0.94
Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. J Mol Biol (2011) 0.93
Analysis of riboswitch structure and function by an energy landscape framework. J Mol Biol (2009) 0.93
Genomic SELEX: a discovery tool for genomic aptamers. Methods (2010) 0.93
Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes. Chem Biol (2014) 0.93
New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res (2011) 0.93
Insights into the regulatory landscape of the lysine riboswitch. J Mol Biol (2012) 0.92
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol (2012) 0.92
Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. J Mol Biol (2011) 0.92
Single-molecule studies of the lysine riboswitch reveal effector-dependent conformational dynamics of the aptamer domain. Biochemistry (2012) 0.91
Constitutive regulatory activity of an evolutionarily excluded riboswitch variant. J Biol Chem (2011) 0.91
Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing. J Mol Biol (2008) 0.91
Evolutionary evidence for alternative structure in RNA sequence co-variation. PLoS Comput Biol (2013) 0.91
A large-scale association study for nanoparticle C60 uncovers mechanisms of nanotoxicity disrupting the native conformations of DNA/RNA. Nucleic Acids Res (2012) 0.90
Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. RNA (2008) 0.90
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch. J Mol Biol (2013) 0.89
Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA (2011) 0.88
Nucleic acid aptamers: research tools in disease diagnostics and therapeutics. Biomed Res Int (2014) 0.88
Engineering cooperative tecto-RNA complexes having programmable stoichiometries. Nucleic Acids Res (2010) 0.87
Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods (2010) 0.87
Convergent donor and acceptor substrate utilization among kinase ribozymes. Nucleic Acids Res (2010) 0.87
Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch. Nucleic Acids Res (2009) 0.86
The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain. RNA Biol (2014) 0.86
Protein design for pathway engineering. J Struct Biol (2013) 0.85
Transport of magnesium by a bacterial Nramp-related gene. PLoS Genet (2014) 0.84
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature (2006) 4.22
Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol (2008) 3.13
Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol (2006) 2.81
Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem (2008) 2.27
Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure (2010) 2.02
Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure (2009) 1.84
Ligand-dependent folding of the three-way junction in the purine riboswitch. RNA (2008) 1.77
Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol (2011) 1.75
A general strategy to solve the phase problem in RNA crystallography. Structure (2007) 1.74
Structural insights into the signal recognition particle. Annu Rev Biochem (2004) 1.64
A general method for rapid and nondenaturing purification of RNAs. RNA (2004) 1.57
Mutational analysis of the purine riboswitch aptamer domain. Biochemistry (2007) 1.44
B12 cofactors directly stabilize an mRNA regulatory switch. Nature (2012) 1.38
The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure (2011) 1.36
Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol (2009) 1.33
A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J Mol Biol (2008) 1.31
A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta (2009) 1.29
Telomere capping proteins are structurally related to RPA with an additional telomere-specific domain. Proc Natl Acad Sci U S A (2009) 1.19
Modified pyrimidines specifically bind the purine riboswitch. J Am Chem Soc (2006) 1.19
Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA (2010) 1.10
Novel ligands for a purine riboswitch discovered by RNA-ligand docking. Chem Biol (2011) 1.09
Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth Biol (2013) 1.04
The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity. Nucleic Acids Res (2006) 1.01
Determining structures of RNA aptamers and riboswitches by X-ray crystallography. Methods Mol Biol (2009) 1.01
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection. Nucleic Acids Res (2011) 0.99
Mix-and-match riboswitches. ACS Chem Biol (2006) 0.98
Strategies in RNA crystallography. Methods Enzymol (2009) 0.97
Monitoring RNA-ligand interactions using isothermal titration calorimetry. Methods Mol Biol (2009) 0.97
Riboswitches: fold and function. Chem Biol (2006) 0.96
Structural basis for diversity in the SAM clan of riboswitches. Proc Natl Acad Sci U S A (2014) 0.92
Insights into the regulatory landscape of the lysine riboswitch. J Mol Biol (2012) 0.92
Single-molecule studies of the lysine riboswitch reveal effector-dependent conformational dynamics of the aptamer domain. Biochemistry (2012) 0.91
Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch. J Mol Biol (2013) 0.89
Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.89
Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res (2013) 0.89
Preparation of group I introns for biochemical studies and crystallization assays by native affinity purification. PLoS One (2009) 0.83
Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch. J Am Chem Soc (2014) 0.82
The Cech Symposium: a celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom. RNA (2008) 0.81
Quantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping. RNA (2003) 0.79
Curse of the hairpin loop. Structure (2004) 0.78
Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex. J Biol Chem (2009) 0.78