Metabolite recognition principles and molecular mechanisms underlying riboswitch function

Serganov, Alexander; Patel, Dinshaw J.

doi:10.1146/annurev-biophys-101211-113224

Cited by 161RNA and protein synthesis mechanismsRNA modifications and cancerDNA and Nucleic Acid Chemistry

Metabolite recognition principles and molecular mechanisms underlying riboswitch function

Open access

Serganov, Alexander, Patel, Dinshaw J.·2012·Annual Review of Biophysics

DOI 10.1146/annurev-biophys-101211-113224PMC PMC4696762

Open this paper in CoChat — free account

Abstract

Riboswitches are mRNA elements capable of modulating gene expression in response to specific binding by cellular metabolites. Riboswitches exert their function through the interplay of alternative ligand-free and ligand-bound conformations of the metabolite-sensing domain, which in turn modulate the formation of adjacent gene expression controlling elements. X-ray crystallography and NMR spectroscopy have determined three-dimensional structures of virtually all the major riboswitch classes in the ligand-bound state and, for several riboswitches, in the ligand-free state. The resulting spatial topologies have demonstrated the wide diversity of riboswitch folds and revealed structural principles for specific recognition by cognate metabolites. The available three-dimensional information, supplemented by structure-guided biophysical and biochemical experimentation, has led to an improved understanding of how riboswitches fold, what RNA conformations are required for ligand recognition, and how ligand binding can be transduced into gene expression modulation. These studies have greatly facilitated the dissection of molecular mechanisms underlying riboswitch action and should in turn guide the anticipated development of tools for manipulating gene regulatory circuits.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1146/annurev-biophys-101211-113224

Cites

136 of 136 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Direct recognition of amino acids by RNA molecules survives in other functional spheres of modern cells, in particular, as amino acid-binding riboswitches.
“It seems interesting to note that, although direct recognition of amino acids by RNA molecules seems to be banished from the modern translation system, it survives in other functional spheres of modern cells, in particular, as amino acid-binding riboswitches [96,97].”
From Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code (2017) · cites this paper as [97]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The role of dynamic conformational ensembles in biomolecular recognition
Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008 · see citing works
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
Winkler, W. C., Nahvi, A., & Breaker, R. R. (2002) · Nature · doi:10.1038/nature01145 · Cited by 1,241 · see citing works
Control of gene expression by a natural metabolite-responsive ribozyme
Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., & Breaker, R. R. (2004) · Nature · doi:10.1038/nature02362 · Cited by 953 · see citing works
Genetic Control by a Metabolite Binding mRNA
Nahvi, A., Sudarsan, N., Ebert, M. S., Zou, X., Brown, K. L., & Breaker, R. R. (2002) · Chemistry & Biology · doi:10.1016/s1074-5521(02)00224-7 · Cited by 802 · see citing works
RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE)
Merino, E. J., Wilkinson, K. A., Coughlan, J. L., & Weeks, K. M. (2005) · Journal of the American Chemical Society · doi:10.1021/ja043822v · Cited by 791 · see citing works
The kink‐turn: a new RNA secondary structure motif
Klein, D. J., Schmeing, T. M., Moore, P. B., & Steitz, T. A. (2001) · The EMBO Journal · doi:10.1093/emboj/20.15.4214 · Cited by 740 · see citing works
Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria
Mandal, M., Boese, B. J., Barrick, J. E., Winkler, W. C., & Breaker, R. R. (2003) · Cell · doi:10.1016/s0092-8674(03)00391-x · Cited by 729 · see citing works
REGULATION OF BACTERIAL GENE EXPRESSION BY RIBOSWITCHES
Winkler, W. C., & Breaker, R. R. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.030804.121336 · Cited by 725 · see citing works
Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP
Sudarsan, N., Lee, E. R., Zasha Weinberg, A., Moy, R. H., Kim, J. N., Link, K. H., & Breaker, R. R. (2008) · Science · doi:10.1126/science.1159519 · Cited by 720 · see citing works
An mRNA structure that controls gene expression by binding FMN
Winkler, W. C., Cohen‐Chalamish, S., & Breaker, R. R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212628899 · Cited by 698 · see citing works
Sensing Small Molecules by Nascent RNA
Mironov, A. S., Gusarov, I., Rafikov, R., Errais, L. L., Shatalin, K. Y., Kreneva, R. A., Perumov, D. A., & Nudler, E. (2002) · Cell · doi:10.1016/s0092-8674(02)01134-0 · Cited by 682 · see citing works
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B., & Steitz, T. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.081082398 · Cited by 659 · see citing works
The riboswitch control of bacterial metabolism
Nudler, E. (2003) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2003.11.004 · Cited by 574 · see citing works
Structural Basis for Discriminative Regulation of Gene Expression by Adenine- and Guanine-Sensing mRNAs
Serganov, A., Yuan, Y.-R., Pikovskaya, O., Polonskaia, A., Malinina, L. V., Phan, A. T., Höbartner, C., Micura, R., Breaker, R. R., & Patel, D. J. (2004) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.11.018 · Cited by 560 · see citing works
Self-citation
The Structural and Functional Diversity of Metabolite-Binding Riboswitches
Roth, A., & Breaker, R. R. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.78.070507.135656 · Cited by 555 · see citing works
Relationship between internucleotide linkage geometry and the stability of RNA
Soukup, G. A., & Breaker, R. R. (1999) · RNA · doi:10.1017/s1355838299990891 · Cited by 549 · see citing works
A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression
Mandal, M., Lee, M. N., Barrick, J. E., Zasha Weinberg, A., Emilsson, G. M., Ruzzo, W. L., & Breaker, R. R. (2004) · Science · doi:10.1126/science.1100829 · Cited by 545 · see citing works
Adenine riboswitches and gene activation by disruption of a transcription terminator
Mandal, M., & Breaker, R. R. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb710 · Cited by 514 · see citing works
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
Batey, R., Gilbert, S. D., & Montange, R. K. (2004) · Nature · doi:10.1038/nature03037 · Cited by 509 · see citing works
The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch
Wickiser, J. K., Winkler, W. C., Breaker, R. R., & Crothers, D. M. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.02.032 · Cited by 483 · see citing works
An mRNA structure that controls gene expression by binding S-adenosylmethionine
Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E., & Breaker, R. R. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb967 · Cited by 458 · see citing works
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R., & Patel, D. J. (2006) · Nature · doi:10.1038/nature04740 · Cited by 443 · see citing works
Self-citation
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins
Serganov, A., & Patel, D. J. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2172 · Cited by 438 · see citing works
Self-citation
Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride
Baker, J. L., Sudarsan, N., Zasha Weinberg, A., Roth, A., Stockbridge, R. B., & Breaker, R. R. (2011) · Science · doi:10.1126/science.1215063 · Cited by 435 · see citing works
Metabolite-binding RNA domains are present in the genes of eukaryotes
Sudarsan, N., Barrick, J. E., & Breaker, R. R. (2003) · RNA · doi:10.1261/rna.5090103 · Cited by 418 · see citing works
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
Montange, R. K., & Batey, R. (2006) · Nature · doi:10.1038/nature04819 · Cited by 405 · see citing works
Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain
Correll, C. C., Freeborn, B., Moore, P. B., & Steitz, T. A. (1997) · Cell · doi:10.1016/s0092-8674(00)80457-2 · Cited by 393 · see citing works
Structure and Mechanism of a Metal-Sensing Regulatory RNA
Dann, C. E., Wakeman, C. A., Sieling, C. L., Baker, S. C., Irnov, I., & Winkler, W. C. (2007) · Cell · doi:10.1016/j.cell.2007.06.051 · Cited by 386 · see citing works
Riboswitches: Emerging Themes in RNA Structure and Function
Montange, R. K., & Batey, R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.130000 · Cited by 386 · see citing works
Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers
Greenleaf, W. J., Frieda, K. L., Foster, D. A. N., Woodside, M. T., & Block, S. M. (2008) · Science · doi:10.1126/science.1151298 · Cited by 385 · see citing works
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
Zasha Weinberg, A., Wang, J. X., Bogue, J. T., Yang, J., Corbino, K. A., Moy, R. H., & Breaker, R. R. (2010) · Genome biology · doi:10.1186/gb-2010-11-3-r31 · Cited by 380 · see citing works
A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes
Loh, E., Dussurget, O., Gripenland, J., Vaitkevicius, K., Tiensuu, T., Mandin, P., Repoila, F., Buchrieser, C., Cossart, P., & Johansson, J. (2009) · Cell · doi:10.1016/j.cell.2009.08.046 · Cited by 379 · see citing works
Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate
Klein, D. J., & Ferré-D’Amaré, A. R. (2006) · Science · doi:10.1126/science.1129666 · Cited by 377 · see citing works
An mRNA structure in bacteria that controls gene expression by binding lysinePreprint
Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S., & Breaker, R. R. (2003) · Genes & Development · doi:10.1101/gad.1140003 · Cited by 357 · see citing works
An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger
Lee, E. R., Baker, J. L., Zasha Weinberg, A., Sudarsan, N., & Breaker, R. R. (2010) · Science · doi:10.1126/science.1190713 · Cited by 348 · see citing works
Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand
Thore, S., Leibundgut, M., & Ban, N. (2006) · Science · doi:10.1126/science.1128451 · Cited by 345 · see citing works
Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes
Nahvi, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh167 · Cited by 327 · see citing works
An RNA Sensor for Intracellular Mg2+
Cromie, M. J., Shi, Y., Latifi, T. N., & Groisman, E. A. (2006) · Cell · doi:10.1016/j.cell.2006.01.043 · Cited by 325 · see citing works
RNA dynamics: it is about time
Al‐Hashimi, H. M., & Walter, N. G. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.04.004 · Cited by 323 · see citing works
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch
Serganov, A., Huang, L., & Patel, D. J. (2009) · Nature · doi:10.1038/nature07642 · Cited by 290 · see citing works
Self-citation
Structural basis of ligand binding by a c-di-GMP riboswitch
Smith, K. D., Lipchock, S. V., Ames, T. D., Wang, J., Breaker, R. R., & Strobel, S. A. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1702 · Cited by 285 · see citing works
Folding of the Adenine Riboswitch
Lemay, J., Penedo, J. C., Tremblay, R., Lilley, D. M. J., & Lafontaine, D. A. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.06.010 · Cited by 282 · see citing works
The Kinetics of Ligand Binding by an Adenine-Sensing Riboswitch
Wickiser, J. K., Cheah, M. T., Breaker, R. R., & Crothers, D. M. (2005) · Biochemistry · doi:10.1021/bi051008u · Cited by 280 · see citing works
tRNA as a positive regulator of transcription antitermination in B. subtilis
Grundy, F. J., & Henkin, T. M. (1993) · Cell · doi:10.1016/0092-8674(93)80049-k · Cited by 273 · see citing works
Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor
Cochrane, J. C., Lipchock, S. V., & Strobel, S. A. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.12.005 · Cited by 267 · see citing works
Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions
Sudarsan, N., Hammond, M. C., Block, K. F., Welz, R., Barrick, J. E., Roth, A., & Breaker, R. R. (2006) · Science · doi:10.1126/science.1130716 · Cited by 264 · see citing works
Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain
Gilbert, S. D., Stoddard, C. D., Wise, S. J., & Batey, R. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.04.003 · Cited by 263 · see citing works
Structure of the SAM-II riboswitch bound to S-adenosylmethionine
Gilbert, S. D., Rambo, R. P., Tyne, D. V., & Batey, R. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1371 · Cited by 255 · see citing works
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition
Edwards, T. E., & Ferré-D’Amaré, A. R. (2006) · Structure · doi:10.1016/j.str.2006.07.008 · Cited by 252 · see citing works
Structural insights into amino acid binding and gene control by a lysine riboswitch
Serganov, A., Huang, L., & Patel, D. J. (2008) · Nature · doi:10.1038/nature07326 · Cited by 251 · see citing works
Self-citation
The riboswitch-mediated control of sulfur metabolism in bacteria
Epshtein, V., Mironov, A. S., & Nudler, E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0531307100 · Cited by 250 · see citing works
Transcription termination control of the S box system: Direct measurement of S -adenosylmethionine by the leader RNA
McDaniel, B. A., Grundy, F. J., Artsimovitch, I., & Henkin, T. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630422100 · Cited by 246 · see citing works
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain
Roth, A., Winkler, W. C., Regulski, E. E., Lee, B. W. K., Lim, J., Jona, I., Barrick, J. E., Ritwik, A., Kim, J. N., Welz, R., et al. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1224 · Cited by 242 · see citing works
Mechanism of mRNA destabilization by the glmS ribozymePreprint
Collins, J. A., Irnov, I., Baker, S. C., & Winkler, W. C. (2007) · Genes & Development · doi:10.1101/gad.1605307 · Cited by 237 · see citing works
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria
Corbino, K. A., Barrick, J. E., Lim, J., Welz, R., Tucker, B. J., Puskarz, I., Mandal, M., Rudnick, N. D., & Breaker, R. R. (2005) · Genome biology · doi:10.1186/gb-2005-6-8-r70 · Cited by 236 · see citing works
The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase
Fuchs, R. T., Grundy, F. J., & Henkin, T. M. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1059 · Cited by 204 · see citing works
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
Kulshina, N., Baird, N., & Ferré-D’Amaré, A. R. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1701 · Cited by 197 · see citing works
Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain
Stoddard, C. D., Montange, R. K., Hennelly, S. P., Rambo, R. P., Sanbonmatsu, K. Y., & Batey, R. (2010) · Structure · doi:10.1016/j.str.2010.04.006 · Cited by 193 · see citing works
Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element
Garst, A. D., Heroux, A., Rambo, R. P., & Batey, R. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.c800120200 · Cited by 189 · see citing works
The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes
Grundy, F. J., Lehman, S. C., & Henkin, T. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2133705100 · Cited by 186 · see citing works
The Dynamic Nature of RNA as Key to Understanding Riboswitch Mechanisms
Haller, A., Soulière, M. F., & Micura, R. (2011) · Accounts of Chemical Research · doi:10.1021/ar200035g · Cited by 184 · see citing works
Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms
Lemay, J., Desnoyers, G., Blouin, S., Heppell, B., Bastet, L., St-Pierre, P., Massé, É., & Lafontaine, D. A. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001278 · Cited by 179 · see citing works
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Rodionov, D. A., Vitreschak, A. G., Mironov, A. A., & Gelfand, M. S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg900 · Cited by 178 · see citing works
Novel Riboswitch Ligand Analogs as Selective Inhibitors of Guanine-Related Metabolic Pathways
Mulhbacher, J., Brouillette, É., Allard, M., Fortier, L., Malouin, F., & Lafontaine, D. A. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000865 · Cited by 176 · see citing works
Ligand‐Induced Folding of the Adenosine Deaminase A‐Riboswitch and Implications on Riboswitch Translational Control
Rieder, R., Lang, K., Graber, D., & Micura, R. (2007) · ChemBioChem · doi:10.1002/cbic.200700057 · Cited by 175 · see citing works
Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase
Klein, D. J., Edwards, T. E., & Ferré-D’Amaré, A. R. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1563 · Cited by 175 · see citing works
Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism
Lu, C., Smith, A. M., Fuchs, R. T., Ding, F., Rajashankar, K. R., Henkin, T. M., & Ke, A. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1494 · Cited by 171 · see citing works
Reengineering orthogonally selective riboswitches
Dixon, N., Duncan, J. N., Geerlings, T. H., Dunstan, M. S., McCarthy, J. E. G., Leys, D., & Micklefield, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911209107 · Cited by 169 · see citing works
Conformational capture of the SAM-II riboswitch
Haller, A., Rieder, U., Aigner, M., Blanchard, S. C., & Micura, R. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.562 · Cited by 166 · see citing works
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism
Regulski, E. E., Moy, R. H., Zasha Weinberg, A., Barrick, J. E., Yao, Z., Ruzzo, W. L., & Breaker, R. R. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06208.x · Cited by 162 · see citing works
Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach
Lang, K., Rieder, R., & Micura, R. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm580 · Cited by 154 · see citing works
Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
Noeske, J., Buck, J., Fürtig, B., Nasiri, H. R., Schwalbe, H., & Wöhnert, J. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl1094 · Cited by 147 · see citing works
Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch
Huang, L., Serganov, A., & Patel, D. J. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.11.026 · Cited by 147 · see citing works
Self-citation
Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules
Zhang, J., Lau, M. W. L., & Ferré-D’Amaré, A. R. (2010) · Biochemistry · doi:10.1021/bi1012645 · Cited by 146 · see citing works
An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs
Noeske, J., Richter, C. P., Grundl, M. A., Nasiri, H. R., Schwalbe, H., & Wöhnert, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406347102 · Cited by 146 · see citing works
Ligand Requirements for glmS Ribozyme Self-Cleavage
McCarthy, T. J., Plog, M. A., Floy, S. A., Jansen, J. A., Strauss-Soukup, J. K., & Soukup, G. A. (2005) · Chemistry & Biology · doi:10.1016/j.chembiol.2005.09.006 · Cited by 146 · see citing works
Riboswitches: small-molecule recognition by gene regulatory RNAs
Edwards, T. E., Klein, D. J., & Ferré-D’Amaré, A. R. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.05.004 · Cited by 144 · see citing works
Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA
Kang, M., Peterson, R. D., & Feigon, J. F. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.019 · Cited by 142 · see citing works
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine
Kim, J. N., Roth, A., & Breaker, R. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0705884104 · Cited by 138 · see citing works
Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation
Jenkins, J. L., Krucinska, J., McCarty, R. M., Bandarian, V., & Wedekind, J. E. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.230375 · Cited by 137 · see citing works
Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution
Buck, J., Fürtig, B., Noeske, J., Wöhnert, J., & Schwalbe, H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703182104 · Cited by 135 · see citing works
The Structure of a Tetrahydrofolate-Sensing Riboswitch Reveals Two Ligand Binding Sites in a Single Aptamer
Trausch, J. J., Ceres, P., Reyes, F. E., & Batey, R. (2011) · Structure · doi:10.1016/j.str.2011.06.019 · Cited by 134 · see citing works
Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism
Neupane, K., Yu, H., Foster, D. A. N., Wang, F., & Woodside, M. T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr305 · Cited by 129 · see citing works
Design and Antimicrobial Action of Purine Analogues That Bind Guanine Riboswitches
Kim, J. N., Blount, K., Puskarz, I., Lim, J., Link, K. H., & Breaker, R. R. (2009) · ACS Chemical Biology · doi:10.1021/cb900146k · Cited by 125 · see citing works
Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio cholerae
Lipfert, J., Das, R., Chu, V. B., Kudaravalli, M., Boyd, N., Herschlag, D., & Doniach, S. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.10.022 · Cited by 117 · see citing works
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection
Vicens, Q., Mondragón, E., & Batey, R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr565 · Cited by 116 · see citing works
Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches
Smith, K. D., Shanahan, C. A., Moore, E. L., Simon, A. C., & Strobel, S. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018857108 · Cited by 115 · see citing works
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria
Meyer, M. M., Roth, A., Chervin, S. M., Garcia, G. A., & Breaker, R. R. (2008) · RNA · doi:10.1261/rna.937308 · Cited by 113 · see citing works
A Bacterial mRNA Leader that Employs Different Mechanisms to Sense Disparate Intracellular Signals
Park, S.-Y., Cromie, M. J., Lee, E., & Groisman, E. A. (2010) · Cell · doi:10.1016/j.cell.2010.07.046 · Cited by 113 · see citing works
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteineThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.
Wang, J. X., & Breaker, R. R. (2008) · Biochemistry and Cell Biology · doi:10.1139/o08-008 · Cited by 112 · see citing works
Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking
Daldrop, P., Reyes, F. E., Robinson, D. A., Hammond, C. M., Lilley, D. M. J., Batey, R., & Brenk, R. (2011) · Chemistry & Biology · doi:10.1016/j.chembiol.2010.12.020 · Cited by 112 · see citing works
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches
Zasha Weinberg, A., Regulski, E. E., Hammond, M. C., Barrick, J. E., Yao, Z., Ruzzo, W. L., & Breaker, R. R. (2008) · RNA · doi:10.1261/rna.988608 · Cited by 111 · see citing works
Molecular insights into the ligand-controlled organization of the SAM-I riboswitch
Heppell, B., Blouin, S., Dussault, A.-M., Mulhbacher, J., Ennifar, E., Penedo, J. C., & Lafontaine, D. A. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.563 · Cited by 110 · see citing works
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria
Poiata, E., Meyer, M. M., Ames, T. D., & Breaker, R. R. (2009) · RNA · doi:10.1261/rna.1824209 · Cited by 108 · see citing works
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions
Roth, A., Nahvi, A., Lee, M. N., Jona, I., & Breaker, R. R. (2006) · RNA · doi:10.1261/rna.2266506 · Cited by 108 · see citing works
Real-time multidimensional NMR follows RNA folding with second resolution
Lee, M., Gal, M., Frydman, L., & Varani, G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001195107 · Cited by 105 · see citing works
Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch
Butler, E. B., Xiong, Y., Wang, J., & Strobel, S. A. (2011) · Chemistry & Biology · doi:10.1016/j.chembiol.2011.01.013 · Cited by 104 · see citing works
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
Baird, N., & Ferré-D’Amaré, A. R. (2010) · RNA · doi:10.1261/rna.1852310 · Cited by 104 · see citing works
Folding of a transcriptionally acting PreQ 1 riboswitch
Rieder, U., Kreutz, C., & Micura, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914925107 · Cited by 103 · see citing works
A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate
Ames, T. D., Rodionov, D. A., Zasha Weinberg, A., & Breaker, R. R. (2010) · Chemistry & Biology · doi:10.1016/j.chembiol.2010.05.020 · Cited by 103 · see citing works
Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch
Thore, S., Frick, C., & Ban, N. (2008) · Journal of the American Chemical Society · doi:10.1021/ja801708e · Cited by 101 · see citing works
The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain
Spitale, R. C., Torelli, A. T., Krucinska, J., Bandarian, V., & Wedekind, J. E. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.c900024200 · Cited by 100 · see citing works
Riboswitch-mediated control of gene expression in eukaryotes
Wachter, A. (2010) · RNA Biology · doi:10.4161/rna.7.1.10489 · Cited by 100 · see citing works
Ligand-dependent folding of the three-way junction in the purine riboswitch
Stoddard, C. D., Gilbert, S. D., & Batey, R. (2008) · RNA · doi:10.1261/rna.736908 · Cited by 99 · see citing works
Bacterial aptamers that selectively bind glutamine
Ames, T. D., & Breaker, R. R. (2011) · RNA Biology · doi:10.4161/rna.8.1.13864 · Cited by 96 · see citing works
Evidence for Preorganization of the glmS Ribozyme Ligand Binding Pocket
Hampel, K. J., & Tinsley, M. M. (2006) · Biochemistry · doi:10.1021/bi060337z · Cited by 95 · see citing works
Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism
Ottink, O. M., Rampersad, S. M., Tessari, M., Zaman, G. J. R., Heus, H. A., & Wijmenga, S. S. (2007) · RNA · doi:10.1261/rna.635307 · Cited by 90 · see citing works
The UA_handle: a versatile submotif in stable RNA architectures†
Jaeger, L., Verzemnieks, E., & Geary, C. W. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn911 · Cited by 87 · see citing works
The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo
Watson, P. Y., & Fedor, M. J. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1989 · Cited by 86 · see citing works
Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch
Pikovskaya, O., Polonskaia, A., Patel, D. J., & Serganov, A. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.631 · Cited by 81 · see citing works
Self-citation
On the occurrence of the T-loop RNA folding motif in large RNA molecules
Krasilnikov, A. S., & Mondragón, A. (2003) · RNA · doi:10.1261/rna.2202703 · Cited by 81 · see citing works
Structural basis for recognition ofS-adenosylhomocysteine by riboswitches
Edwards, A. L., Reyes, F. E., Heroux, A., & Batey, R. (2010) · RNA · doi:10.1261/rna.2341610 · Cited by 81 · see citing works
Requirement of Helix P2.2 and Nucleotide G1 for Positioning the Cleavage Site and Cofactor of the glmS Ribozyme
Klein, D. J., Wilkinson, S. R., Been, M. D., & Ferré-D’Amaré, A. R. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.07.062 · Cited by 78 · see citing works
Chemical basis of glycine riboswitch cooperativity
Kwon, M., & Strobel, S. A. (2007) · RNA · doi:10.1261/rna.771608 · Cited by 75 · see citing works
Ligand recognition determinants of guanine riboswitches
Mulhbacher, J., & Lafontaine, D. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm572 · Cited by 73 · see citing works
Core requirements of the adenine riboswitch aptamer for ligand binding
Lemay, J., & Lafontaine, D. A. (2007) · RNA · doi:10.1261/rna.142007 · Cited by 72 · see citing works
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs
Nagaswamy, U., & Fox, G. E. (2002) · RNA · doi:10.1017/s135583820202006x · Cited by 72 · see citing works
Differential Analogue Binding by Two Classes of c-di-GMP Riboswitches
Shanahan, C. A., Gaffney, B. L., Jones, R. A., & Strobel, S. A. (2011) · Journal of the American Chemical Society · doi:10.1021/ja204650q · Cited by 67 · see citing works
The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure
Ali, M., Lipfert, J., Seifert, S., Herschlag, D., & Doniach, S. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.11.030 · Cited by 66 · see citing works
A Structural Basis for the Recognition of 2′-Deoxyguanosine by the Purine Riboswitch
Edwards, A. L., & Batey, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.10.074 · Cited by 66 · see citing works
Regulation of magnesium homeostasis in Salmonella: Mg2+ targets the mgtA transcript for degradation by RNase E
Spinelli, S. V., Pontel, L. B., Véscovi, E. G., & Soncini, F. C. (2008) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2008.01065.x · Cited by 65 · see citing works
Multivector Fluorescence Analysis of the xpt Guanine Riboswitch Aptamer Domain and the Conformational Role of Guanine
Brenner, M. D., Scanlan, M. S., Nahas, M. K., Ha, T., & Silverman, S. K. (2010) · Biochemistry · doi:10.1021/bi9019912 · Cited by 64 · see citing works
Trans-acting glmS catalytic riboswitch: Locked and loaded
Tinsley, R. A., Furchak, J. R. W., & Walter, N. G. (2007) · RNA · doi:10.1261/rna.341807 · Cited by 64 · see citing works
Switching the light on plant riboswitches
Bocobza, S. E., & Aharoni, A. (2008) · Trends in Plant Science · doi:10.1016/j.tplants.2008.07.004 · Cited by 59 · see citing works
Characteristics of Ligand Recognition by a glmS Self‐Cleaving Ribozyme
Lim, J., Grove, B. C., Roth, A., & Breaker, R. R. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200602534 · Cited by 57 · see citing works
Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch
Huang, L., Ishibe-Murakami, S., Patel, D. J., & Serganov, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111701108 · Cited by 54 · see citing works
Self-citation
Tuning Riboswitch Regulation through Conformational Selection
Wilson, R. C., Smith, A. M., Fuchs, R. T., Kleckner, I. R., Henkin, T. M., & Foster, M. P. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.10.056 · Cited by 51 · see citing works
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
Huang, W., Kim, J., Jha, S., & Aboul‐ela, F. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp664 · Cited by 50 · see citing works
Insights into Metalloregulation by M-box Riboswitch RNAs via Structural Analysis of Manganese-Bound Complexes
Ramesh, A., Wakeman, C. A., & Winkler, W. C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.01.049 · Cited by 49 · see citing works
Riboswitch structure: an internal residue mimicking the purine ligand
Delfosse, V., Bouchard, P., Bonneau, É., Dagenais, P., Lemay, J., Lafontaine, D. A., & Legault, P. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1080 · Cited by 48 · see citing works
glmS Riboswitch Binding to the Glucosamine-6-phosphate α-Anomer Shifts the pKa toward Neutrality
Davis, J., Dunican, B. F., & Strobel, S. A. (2011) · Biochemistry · doi:10.1021/bi200471c · Cited by 41 · see citing works
Mg2+ facilitates leader peptide translation to induce riboswitch‐mediated transcription termination
Zhao, G., Kong, W., Weatherspoon‐Griffin, N., Clark‐Curtiss, J. E., & Shi, Y. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.66 · Cited by 33 · see citing works
Multiple Metal-Binding Cores Are Required for Metalloregulation by M-box Riboswitch RNAs
Wakeman, C. A., Ramesh, A., & Winkler, W. C. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.033 · Cited by 32 · see citing works
Heterogeneity and Dynamics of the Ligand Recognition Mode in Purine-Sensing Riboswitches
Jain, N., Zhao, L., Liu, J. D., & Xia, T. (2010) · Biochemistry · doi:10.1021/bi1000036 · Cited by 23 · see citing works
Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding
Klawuhn, K., Jansen, J. A., Souchek, J. J., Soukup, G. A., & Strauss-Soukup, J. K. (2010) · ChemBioChem · doi:10.1002/cbic.201000544 · Cited by 22 · see citing works
Constitutive Regulatory Activity of an Evolutionarily Excluded Riboswitch Variant
Tremblay, R., Lemay, J., Blouin, S., Mulhbacher, J., Bonneau, É., Legault, P., Dupont, P., Penedo, J. C., & Lafontaine, D. A. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.229047 · Cited by 21 · see citing works

Flagged first, then by citations

Sorted by citations

A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tailsPreprint
Wilusz, J. E., JnBaptiste, C. K., Lu, L. Y., Kuhn, C., Joshua‐Tor, L., & Sharp, P. A. (2012) · Genes & Development · doi:10.1101/gad.204438.112 · Cited by 487 · see citing works
Riboswitch diversity and distribution
McCown, P. J., Corbino, K. A., Stav, S., Sherlock, M. E., & Breaker, R. R. (2017) · RNA · doi:10.1261/rna.061234.117 · Cited by 467 · see citing works
Regulation of Bacterial Virulence by Csr (Rsm) Systems
Vakulskas, C. A., Potts, A. H., Babitzke, P., Ahmer, B. M. M., & Romeo, T. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00052-14 · Cited by 333 · see citing works
Automated physics-based design of synthetic riboswitches from diverse RNA aptamers
Borujeni, A. E., Mishler, D. M., Wang, J., Huso, W. D., & Salis, H. M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1289 · Cited by 265 · see citing works
Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
Micura, R., & Höbartner, C. (2020) · Chemical Society Reviews · doi:10.1039/d0cs00617c · Cited by 264 · see citing works
Discovering riboswitches: the past and the future
Kavita, K., & Breaker, R. R. (2022) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2022.08.009 · Cited by 255 · see citing works
Imaging metabolite dynamics in living cells using a Spinach-based riboswitch
You, M., Litke, J. L., & Jaffrey, S. R. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1504354112 · Cited by 210 · see citing works
Hierarchy of RNA Functional Dynamics
Mustoe, A. M., Brooks, C. L., & Al‐Hashimi, H. M. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035524 · Cited by 197 · see citing works
Dynamic metabolic engineering: New strategies for developing responsive cell factories
Reizman, I., & Prather, K. L. J. (2015) · Biotechnology Journal · doi:10.1002/biot.201400422 · Cited by 187 · see citing works
Bacterial Riboswitches Cooperatively Bind Ni 2+ or Co 2+ Ions and Control Expression of Heavy Metal Transporters
Furukawa, K., Ramesh, A., Zhou, Z., Zasha Weinberg, A., Vallery, T. K., Winkler, W. C., & Breaker, R. R. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.009 · Cited by 166 · see citing works
Kinetic and Equilibrium Binding Characterization of Aptamers to Small Molecules using a Label-Free, Sensitive, and Scalable Platform
Chang, A. L., McKeague, M., Liang, J. C., & Smolke, C. D. (2014) · Analytical Chemistry · doi:10.1021/ac5001527 · Cited by 140 · see citing works
An Ancient Riboswitch Class in Bacteria Regulates Purine Biosynthesis and One-Carbon Metabolism
Kim, P. B., Nelson, J. W., & Breaker, R. R. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.001 · Cited by 120 · see citing works
Control of bacterial exoelectrogenesis by c-AMP-GMP
Nelson, J. W., Sudarsan, N., Phillips, G. E., Stav, S., Weinberg, C. E., McCown, P. J., & Breaker, R. R. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419264112 · Cited by 116 · see citing works
A New Facet of Vitamin B12: Gene Regulation by Cobalamin-Based Photoreceptors
Padmanabhan, S., Jost, M., Drennan, C. L., & Arnanz, M. E. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-044500 · Cited by 115 · see citing works
Riboswitch distribution, structure, and function in bacteria
Pavlova, N., Kaloudas, D., & Prof. Robert Penchovsky, D. R. N. (2019) · Gene · doi:10.1016/j.gene.2019.05.036 · Cited by 116 · see citing works
Coenzymes and their role in the evolution of life
Kirschning, A. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.201914786 · Cited by 107 · see citing works
Themes and variations in riboswitch structure and function
Peselis, A., & Serganov, A. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.02.012 · Cited by 106 · see citing works
Self-citation
Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life
Wong, J., Ng, S.-K., Mat, W.-K., Hu, T., & Xue, H. (2016) · Life · doi:10.3390/life6010012 · Cited by 93 · see citing works
Structural insights into recognition of c-di-AMP by the ydaO riboswitch
Gao, A., & Serganov, A. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1607 · Cited by 104 · see citing works
Self-citation
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry–related pockets
Ren, A., & Patel, D. J. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1606 · Cited by 104 · see citing works
Self-citation
The ins and outs of lncRNA structure: How, why and what comes next?
Blythe, A. J., Fox, A. H., & Bond, C. S. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.08.009 · Cited by 94 · see citing works
Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA
Wicks, S. L., & Hargrove, A. E. (2019) · Methods · doi:10.1016/j.ymeth.2019.04.018 · Cited by 91 · see citing works
Characterizing Slow Chemical Exchange in Nucleic Acids by Carbon CEST and Low Spin-Lock Field R1ρ NMR Spectroscopy
Zhao, B., Hansen, A. L., & Zhang, Q. (2013) · Journal of the American Chemical Society · doi:10.1021/ja409835y · Cited by 90 · see citing works
A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation MarksPreprint
Patel, D. J. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018754 · Cited by 87 · see citing works
Self-citation
Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code
Koonin, E. (2017) · Life · doi:10.3390/life7020022 · Cited by 85 · see citing works
“It seems interesting to note that, although direct recognition of amino acids by RNA molecules seems to be banished from the modern translation system, it survives in other functional spheres of modern cells, in particular, as amino acid-binding riboswitches [96,97].”
Background
Anti-frameshifting Ligand Reduces the Conformational Plasticity of the SARS Virus Pseudoknot
Ritchie, D. B., Soong, J., Sikkema, W. K. A., & Woodside, M. T. (2014) · Journal of the American Chemical Society · doi:10.1021/ja410344b · Cited by 83 · see citing works
Molecular Mechanisms of Transcription through Single-Molecule Experiments
Dangkulwanich, M., Ishibashi, T., Bintu, L., & Bustamante, C. (2014) · Chemical Reviews · doi:10.1021/cr400730x · Cited by 81 · see citing works
Structure and function of the T‐loop structural motif in noncoding RNAs
Chan, C. W., Chetnani, B., & Mondragón, A. (2013) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1175 · Cited by 74 · see citing works
Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes
Pérez‐González, C., Lafontaine, D. A., & Penedo, J. C. (2016) · Frontiers in Chemistry · doi:10.3389/fchem.2016.00033 · Cited by 73 · see citing works
Nutrient salvaging and metabolism by the intracellular pathogen Legionella pneumophila
Fonseca, M. V., & Swanson, M. S. (2014) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2014.00012 · Cited by 69 · see citing works
Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch
Ren, A., Xue, Y., Peselis, A., Serganov, A., Al‐Hashimi, H. M., & Patel, D. J. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.10.062 · Cited by 67 · see citing works
Self-citation
Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology
Kang, Z., Zhang, C., Zhang, J., Jin, P. K., Zhang, J., Du, G., & Chen, J. (2014) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-014-5569-y · Cited by 61 · see citing works
A Disconnect between High-Affinity Binding and Efficient Regulation by Antifolates and Purines in the Tetrahydrofolate Riboswitch
Trausch, J. J., & Batey, R. (2014) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.11.012 · Cited by 57 · see citing works
Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin
Polaski, J. T., Webster, S. M., Johnson, J. E., & Batey, R. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.787176 · Cited by 56 · see citing works
New molecular engineering approaches for crystallographic studies of large RNAs
Zhang, J., & Ferré-D’Amaré, A. R. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.02.001 · Cited by 55 · see citing works
Recognition of Nucleic Acid Junctions Using Triptycene‐Based Molecules
Barros, S. A., & Chenoweth, D. M. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201407061 · Cited by 55 · see citing works
Using RNA as Molecular Code for Programming Cellular Function
Kushwaha, M., Rostain, W., Prakash, S., Duncan, J. N., & Jaramillo, A. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00297 · Cited by 53 · see citing works
The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
Li, S., Hwang, X. Y., Stav, S., & Breaker, R. R. (2016) · RNA · doi:10.1261/rna.054890.115 · Cited by 52 · see citing works
Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
Palma, F. D., Colizzi, F., & Bussi, G. (2013) · RNA · doi:10.1261/rna.040493.113 · Cited by 50 · see citing works
What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin‐Sensing Riboswitch
Duchardt, E., Schmidtke, S. R., Weigand, J. E., Ohlenschläger, O., Wurm, J., Hammann, C., Suess, B., & Wöhnert, J. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201507365 · Cited by 47 · see citing works
Loop–loop interaction in an adenine-sensing riboswitch: A molecular dynamics study
Allnér, O., Nilsson, L., & Villa, A. (2013) · RNA · doi:10.1261/rna.037549.112 · Cited by 46 · see citing works
Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes
Sherlock, M. E., & Breaker, R. R. (2020) · RNA · doi:10.1261/rna.074997.120 · Cited by 46 · see citing works
Global analysis of riboswitches by small-angle X-ray scattering and calorimetry
Zhang, J., Jones, C. P., & Ferré-D’Amaré, A. R. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.04.014 · Cited by 44 · see citing works
Characterizing excited conformational states of RNA by NMR spectroscopy
Zhao, B., & Zhang, Q. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.02.011 · Cited by 43 · see citing works
Regulatory 3′ Untranslated Regions of Bacterial mRNAs
Ren, G., Guo, X.-P., & Sun, Y. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01276 · Cited by 43 · see citing works
Slow molecular recognition by RNA
Gleitsman, K. R., Sengupta, R. N., & Herschlag, D. (2017) · RNA · doi:10.1261/rna.062026.117 · Cited by 40 · see citing works
Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions
Bou‐Nader, C., & Zhang, J. (2020) · Molecules · doi:10.3390/molecules25122881 · Cited by 41 · see citing works
A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments
Noell, S. E., Hellweger, F. L., Temperton, B., & Giovannoni, S. J. (2023) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00124-22 · Cited by 40 · see citing works
Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism
Ren, A., Rajashankar, K. R., & Patel, D. J. (2015) · Structure · doi:10.1016/j.str.2015.05.016 · Cited by 40 · see citing works
Self-citation
Linking aptamer‐ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design
Aboul‐ela, F., Huang, W., Elrahman, M. A., Boyapati, V., & Li, P. (2015) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1300 · Cited by 39 · see citing works
Intracellular Imaging with Genetically Encoded RNA-Based Molecular Sensors
Sun, Z., Nguyen, T., McAuliffe, K., & You, M. (2019) · Nanomaterials · doi:10.3390/nano9020233 · Cited by 39 · see citing works
Getting to the bottom of lncRNA mechanism: structure–function relationships
Sanbonmatsu, K. Y. (2021) · Mammalian Genome · doi:10.1007/s00335-021-09924-x · Cited by 38 · see citing works
Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer
Duesterberg, V. K., Fischer-Hwang, I., Perez, C. F., Hogan, D. W., & Block, S. M. (2015) · eLife · doi:10.7554/elife.12362 · Cited by 37 · see citing works
Supramolecular Fluorescence Resonance Energy Transfer in Nucleobase‐Modified Fluorogenic RNA Aptamers
Steinmetzger, C., Bäuerlein, C., & Höbartner, C. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.201916707 · Cited by 35 · see citing works
Ligand‐Detected Relaxation Dispersion NMR Spectroscopy: Dynamics of preQ1–RNA Binding
Moschen, T., Wunderlich, C. H., Spitzer, R., Levic, J., Micura, R., Tollinger, M., & Kreutz, C. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201409779 · Cited by 36 · see citing works
Single-molecule chemical denaturation of riboswitches
Dalgarno, P. A., Bordello, J., Morris, R., St-Pierre, P., Dubé, A., Samuel, I. D. W., Lafontaine, D. A., & Penedo, J. C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt128 · Cited by 33 · see citing works
Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy
Ruff, K. M., & Strobel, S. A. (2014) · RNA · doi:10.1261/rna.047266.114 · Cited by 33 · see citing works
NMR characterization of RNA small molecule interactions
Thompson, R. D., Baisden, J. T., & Zhang, Q. (2019) · Methods · doi:10.1016/j.ymeth.2019.05.015 · Cited by 31 · see citing works
Cooperativity, allostery and synergism in ligand binding to riboswitches
Peselis, A., Gao, A., & Serganov, A. (2015) · Biochimie · doi:10.1016/j.biochi.2015.06.028 · Cited by 31 · see citing works
Self-citation
RNA structures are involved in the thermoregulation of bacterial virulence-associated traits
Grosso-Becera, M. V., Servín‐González, L., & Soberón‐Chávez, G. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.04.004 · Cited by 31 · see citing works
The Perturbed Free‐Energy Landscape: Linking Ligand Binding to Biomolecular Folding
Abdelsattar, A. S., Mansour, Y., & Aboul‐ela, F. (2020) · ChemBioChem · doi:10.1002/cbic.202000695 · Cited by 30 · see citing works
Riboswitch Mechanisms: New Tricks for an Old Dog
Ariza‐Mateos, A., Nuthanakanti, A., & Serganov, A. (2021) · Biochemistry (Moscow) · doi:10.1134/s0006297921080071 · Cited by 29 · see citing works
Self-citation
The inorganic chemistry of the cobalt corrinoids – an update
Marques, H. M. (2023) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2023.112154 · Cited by 28 · see citing works
The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
Huang, W., Kim, J., Jha, S., & Aboul‐ela, F. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003069 · Cited by 28 · see citing works
Engineering and characterization of fluorogenic glycine riboswitches
Ketterer, S., Gladis, L., Kozica, A., & Meier, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw465 · Cited by 27 · see citing works
Frozen Accident Pushing 50: Stereochemistry, Expansion and Chance in the Evolution of the Genetic Code
Koonin, E. (2017) · doi:10.20944/preprints201705.0121.v1 · Cited by 85 · see citing works
Probing excited conformational states of nucleic acids by nitrogen CEST NMR spectroscopy
Zhao, B., Baisden, J. T., & Zhang, Q. (2019) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2019.106642 · Cited by 25 · see citing works
Applications of Synchrotron‐Based Spectroscopic Techniques in Studying Nucleic Acids and Nucleic Acid‐Functionalized Nanomaterials
Wu, P., Yu, Y., McGhee, C. E., Tan, L. H., & Lu, Y. (2014) · Advanced Materials · doi:10.1002/adma.201304891 · Cited by 25 · see citing works
Architectures and complex functions of tandem riboswitches
Sherlock, M. E., Higgs, G., Yu, D., Widner, D. L., White, N. A., Sudarsan, N., Sadeeshkumar, H., Perkins, K. R., Arachchilage, G. M., Malkowski, S. N., et al. (2022) · RNA Biology · doi:10.1080/15476286.2022.2119017 · Cited by 24 · see citing works
Ribocentre-switch: a database of riboswitches
Bu, F., Lin, X., Liao, W., Lu, Z., He, Y., Luo, Y., Peng, X., Li, M., Huang, Y., Chen, X., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad891 · Cited by 26 · see citing works
Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding
Chan, C. W., & Mondragón, A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa507 · Cited by 23 · see citing works
Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling
Esquiaqui, J. M., Sherman, E. M., Ye, J., & Fanucci, G. E. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00287 · Cited by 23 · see citing works
Characterizing the Dynamics of the Leader–Linker Interaction in the Glycine Riboswitch with Site-Directed Spin Labeling
Esquiaqui, J. M., Sherman, E. M., Ionescu, S. A., Ye, J., & Fanucci, G. E. (2014) · Biochemistry · doi:10.1021/bi500404b · Cited by 22 · see citing works
The coenzyme/protein pair and the molecular evolution of life
Kirschning, A. (2020) · Natural Product Reports · doi:10.1039/d0np00037j · Cited by 21 · see citing works
Flipping the script: Understanding riboswitches from an alternative perspective
Olenginski, L. T., Spradlin, S., & Batey, R. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.105730 · Cited by 23 · see citing works
Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Torgerson, C. D., Hiller, D. A., Stav, S., & Strobel, S. A. (2018) · RNA · doi:10.1261/rna.067884.118 · Cited by 22 · see citing works
Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses
Dey, A., Yan, S., Tamar Schlick, A., & Laederach, A. (2024) · RNA · doi:10.1261/rna.080035.124 · Cited by 21 · see citing works
Metabolomic analysis of riboswitch containing E. coli recombinant expression system
Muhamadali, H., Yun Xu, A., Morra, R., Trivedi, D. K., Rattray, N. J. W., Dixon, N., & Goodacre, R. (2015) · Molecular BioSystems · doi:10.1039/c5mb00624d · Cited by 21 · see citing works
Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules
Eubanks, C. S., Zhao, B., Patwardhan, N. N., Thompson, R. D., Zhang, Q., & Hargrove, A. E. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b09665 · Cited by 18 · see citing works
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches
Lennon, S. R., & Batey, R. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167585 · Cited by 17 · see citing works
The regulation mechanism of yitJ and metF riboswitches
Gong, S., Wang, Y., & Zhang, W. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4927390 · Cited by 17 · see citing works
RNA Structural Differentiation: Opportunities with Pattern Recognition
Eubanks, C. S., & Hargrove, A. E. (2018) · Biochemistry · doi:10.1021/acs.biochem.8b01090 · Cited by 17 · see citing works
Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity
Satpathi, S., Endoh, T., Podbevšek, P., Plavec, J., & Sugimoto, N. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab189 · Cited by 17 · see citing works
HNRNPA2B1 as a trigger of RNA switch modulates the miRNA-mediated regulation of CDK6
Yin, M., Cheng, M., Liu, C., Wu, K., Xiong, W., Ji, F., Li, Y., & Zhang, B. (2021) · iScience · doi:10.1016/j.isci.2021.103345 · Cited by 17 · see citing works
Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation
Wilt, H. M., Yu, P., Tan, K., Wang, Y., & Stagno, J. R. (2021) · Journal of Structural Biology · doi:10.1016/j.jsb.2021.107703 · Cited by 16 · see citing works
RNA folding kinetics control riboswitch sensitivity in vivo
Bushhouse, D. Z., Fu, J., & Lucks, J. B. (2025) · Nature Communications · doi:10.1038/s41467-024-55601-3 · Cited by 16 · see citing works
Molecular dynamics simulation of the binding process of ligands to the add adenine riboswitch aptamer
Bao, L., Wang, J., & Xiao, Y. (2019) · Physical review. E · doi:10.1103/physreve.100.022412 · Cited by 16 · see citing works
Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling
Angelin‐Bonnet, O., Biggs, P. J., & Vignes, M. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8882-2_15 · Cited by 14 · see citing works
Recognition of cyclic‐di‐ GMP by a riboswitch conducts translational repression through masking the ribosome‐binding site distant from the aptamer domain
Inuzuka, S., Kakizawa, H., Nishimura, K., Naito, T., Miyazaki, K., Furuta, H., Matsumura, S., & Ikawa, Y. (2018) · Genes to Cells · doi:10.1111/gtc.12586 · Cited by 15 · see citing works
AU-Rich Long 3′ Untranslated Region Regulates Gene Expression in Bacteria
Zhao, J., Zhu, H. F., Guo, X.-P., & Sun, Y. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03080 · Cited by 15 · see citing works
Evolution at the Origins of Life?
Schoenmakers, L. L. J., Reydon, T. A. C., & Kirschning, A. (2024) · Life · doi:10.3390/life14020175 · Cited by 14 · see citing works
Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch
Gorle, S., Srinivasan, H., Nanda, S., & Priyakumar, U. D. (2016) · Biochemistry · doi:10.1021/acs.biochem.5b00973 · Cited by 14 · see citing works
ZMP: A Master Regulator of One-Carbon Metabolism
Ducker, G. S., & Rabinowitz, J. D. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.012 · Cited by 13 · see citing works
NMR resonance assignments for the class II GTP binding RNA aptamer in complex with GTP
Wolter, A. C., Duchardt, E., Nasiri, A. H., Hantke, K., Wunderlich, C. H., Kreutz, C., & Wöhnert, J. (2015) · Biomolecular NMR Assignments · doi:10.1007/s12104-015-9646-7 · Cited by 12 · see citing works
Site-Directed Spin-Labeling Strategies and Electron Paramagnetic Resonance Spectroscopy for Large Riboswitches
Esquiaqui, J. M., Sherman, E. M., Ye, J., & Fanucci, G. E. (2014) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-801122-5.00013-1 · Cited by 12 · see citing works
TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches
Aghdam, E. M., Sinn, M., Tarhriz, V., Barzegar, A., Hartig, J. S., & Hejazi, M. S. (2016) · Microbiological Research · doi:10.1016/j.micres.2016.11.003 · Cited by 11 · see citing works
Responsive self-assembly of tectoRNAs with loop–receptor interactions from the tetrahydrofolate (THF) riboswitch
Mitchell, C., Polanco, J. A., DeWald, L., Kress, D., Jaeger, L., & Grabow, W. W. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz304 · Cited by 11 · see citing works
Advances in chaperone-assisted RNA crystallography using synthetic antibodies
Banna, H. A., Das, N., Ojha, M., & Koirala, D. (2023) · BBA Advances · doi:10.1016/j.bbadva.2023.100101 · Cited by 11 · see citing works
RNA-based antibacterial agents: Mechanisms, functional insights, and challenges in therapeutic development
Abavisani, M., Sajjadi, S. M., Ebadpour, N., Kesharwani, P., Karav, S., & Sahebkar, A. (2025) · Chemical Engineering Journal · doi:10.1016/j.cej.2025.165777 · Cited by 10 · see citing works
Structural insights into translation regulation by the THF-II riboswitch
Xu, L., Xiao, Y., Zhang, J., & Fang, X. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1257 · Cited by 10 · see citing works

Molecular recognition and function of riboswitches
Serganov, A., & Patel, D. J. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.04.005 · Cited by 108 · see citing works
Self-citation
Themes and variations in riboswitch structure and function
Peselis, A., & Serganov, A. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.02.012 · Cited by 106 · see citing works
Self-citation
Determination of riboswitch structures: Light at the end of the tunnel?
Serganov, A. (2010) · RNA Biology · doi:10.4161/rna.7.1.10756 · Cited by 38 · see citing works
Self-citation
The long and the short of riboswitches
Serganov, A. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.02.002 · Cited by 111 · see citing works
Self-citation
Long-Range Interactions in Riboswitch Control of Gene Expression
Jones, C. P., & Ferré-D’Amaré, A. R. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-034042 · Cited by 77 · see citing works

Authors: Serganov, A., & Patel, D. J.
Affiliations: New York University (US)
Memorial Sloan Kettering Cancer Center (US)
ORCID: Serganov, Alexander
Patel, Dinshaw J.
Venue: Annual Review of Biophysics
Publisher: Annual Reviews
Published: 2012-06-09
Volume: 41
Issue: 1
Pages: 343-370
ISSN: 1936-122X (ISSN-L)
1936-1238
DOI: 10.1146/annurev-biophys-101211-113224
PMC: PMC4696762
OpenAlex: W2129215648
Cited by: 160
References: 136
Citations by year: 2026: 4 · 2025: 6 · 2024: 8 · 2023: 8 · 2022: 10 · 2021: 6 · 2020: 13 · 2019: 12 · 2018: 9 · 2017: 10 · 2016: 13 · 2015: 24 · 2014: 27 · 2013: 9 · 2012: 1
FWCI: 1.78
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Annual Review of Biophysics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Cancer Institute (P30CA008748)
National Institute of General Medical Sciences (P41GM066354, GM 66354, R01GM034504)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords: riboswitches, ligand binding, RNA conformational change, gene expression regulation, RNA folding, ligand-free state, ligand-bound state, riboswitch structure, RNA-ligand interactions, gene regulatory circuits
MeSH terms: Bacteria, Ligands, Nucleic Acid Conformation, RNA, Messenger, Gene Expression Regulation, Bacterial, Crystallography, X-Ray, Riboswitch

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Metabolite recognition principles and molecular mechanisms underlying riboswitch function

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Self-check

Cites

Cited by

Related

Record

About these checks