Published in Nucleic Acids Res on November 19, 2010
Molecular recognition and function of riboswitches. Curr Opin Struct Biol (2012) 1.13
Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys (2012) 1.12
RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn. Structure (2011) 1.11
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J Am Chem Soc (2012) 0.98
Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure? Bioarchitecture (2012) 0.95
The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch. Nucleic Acids Res (2012) 0.94
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol (2012) 0.92
Common themes and differences in SAM recognition among SAM riboswitches. Biochim Biophys Acta (2014) 0.82
The impact of a ligand binding on strand migration in the SAM-I riboswitch. PLoS Comput Biol (2013) 0.81
Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch. RNA (2012) 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
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
Fluorescence monitoring of riboswitch transcription regulation using a dual molecular beacon assay. Nucleic Acids Res (2013) 0.78
A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol (2015) 0.77
Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. Wiley Interdiscip Rev RNA (2015) 0.76
A magnesium-induced triplex pre-organizes the SAM-II riboswitch. PLoS Comput Biol (2017) 0.75
Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism. RNA (2017) 0.75
Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat Chem Biol (2017) 0.75
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature (2002) 8.14
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc (2005) 6.46
Relationship between internucleotide linkage geometry and the stability of RNA. RNA (1999) 5.01
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature (2006) 4.22
Folding of the adenine riboswitch. Chem Biol (2006) 3.95
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
An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev (2003) 3.37
The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol (1998) 3.25
The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry (2005) 2.98
The riboswitch-mediated control of sulfur metabolism in bacteria. Proc Natl Acad Sci U S A (2003) 2.83
Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc Natl Acad Sci U S A (2003) 2.68
The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA (2001) 2.40
Genetic control by metabolite-binding riboswitches. Chembiochem (2003) 2.32
Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. Chembiochem (2007) 2.12
The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA (2004) 2.08
Mapping nucleic acid structure by hydroxyl radical cleavage. Curr Opin Chem Biol (2005) 2.06
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc Natl Acad Sci U S A (2003) 1.75
A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control. RNA (2007) 1.73
Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro. J Bacteriol (2007) 1.73
Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism. RNA (2007) 1.70
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA (2010) 1.58
Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot. Biochemistry (2008) 1.49
Melting and premelting transitions of an oligomer measured by DNA base fluorescence and absorption. Biochemistry (1994) 1.41
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell (2008) 1.38
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem Cell Biol (2008) 1.35
Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol (2009) 1.33
Chemical probing of RNA by nucleotide analog interference mapping. Methods Enzymol (2000) 1.33
A tertiary structural element in S box leader RNAs is required for S-adenosylmethionine-directed transcription termination. Mol Microbiol (2005) 1.29
Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry (2004) 1.26
The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA. J Mol Biol (2008) 1.21
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
Identification of a mutation in the Bacillus subtilis S-adenosylmethionine synthetase gene that results in derepression of S-box gene expression. J Bacteriol (2006) 0.99
Structure-function relationships in RNA and RNP enzymes: recent advances. Biopolymers (2007) 0.91
Less isn't always more. RNA (2003) 0.90
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature (2010) 2.85
Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure (2010) 2.02
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res (2010) 1.95
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA (2010) 1.91
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res (2012) 1.58
Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys (2012) 1.12
Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol (2013) 1.07
Excited states of ribosome translocation revealed through integrative molecular modeling. Proc Natl Acad Sci U S A (2011) 1.04
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J Am Chem Soc (2012) 0.98
Rise of the RNA machines: exploring the structure of long non-coding RNAs. J Mol Biol (2013) 0.98
Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. J Mol Biol (2012) 0.96
Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure? Bioarchitecture (2012) 0.95
The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch. Nucleic Acids Res (2012) 0.94
Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. J Am Chem Soc (2010) 0.93
Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. J Am Chem Soc (2011) 0.91
Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys (2013) 0.87
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. J Struct Biol (2011) 0.86
Tackling structures of long noncoding RNAs. Int J Mol Sci (2013) 0.82
3S: shotgun secondary structure determination of long non-coding RNAs. Methods (2013) 0.82