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Ribozyme applications

Publications

This page list the reviews and articles about riboswitches. Click into different sections:





Reviews

Year Author Title Journal
2003 Winkler, W. C. & Breaker, R. R. Genetic control by metabolite-binding riboswitches. Chembiochem
2003 Lai E. C. RNA sensors and riboswitches: self-regulating messages. Curr Biol
2004 Mandal, M. & Breaker, R. R. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol
2004 Nudler, E., & Mironov, A. S. The riboswitch control of bacterial metabolism. Trends Biochem Sci
2004 Batey, R. T., Gilbert, S. D., & Montange, R. K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature
2004 Vitreschak, A. G., Rodionov, D. A., Mironov, A. A., & Gelfand, M. S. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet
2004 Templeton, G. W., & Moorhead, G. B. A renaissance of metabolite sensing and signaling: from modular domains to riboswitches. Plant Cell
2004 Abreu-Goodger, C., Ontiveros-Palacios, N., Ciria, R., & Merino, E. Conserved regulatory motifs in bacteria: riboswitches and beyond. Trends Genet
2005 Winkler, W. C. & Breaker, R. R. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol
2005 Tucker, B. J. & Breaker, R. R. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol
2005 Winkler W. C. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol
2006 Gilbert, S. D., Montange, R. K., Stoddard, C. D., & Batey, R. T. Structural studies of the purine and SAM binding riboswitches. Cold Spring Harb Symp Quant Biol
2006 Blount, K. F. & Breaker, R. R. Riboswitches as antibacterial drug targets. Nat. Biotechnol
2006 Grundy, F. J., & Henkin, T. M. From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements. Crit Rev Biochem Mol Biol
2006 Nudler E. Flipping riboswitches. Cell
2006 Henkin, T. M., & Grundy, F. J. Sensing metabolic signals with nascent RNA transcripts: the T box and S box riboswitches as paradigms. Cold Spring Harb Symp Quant Biol
2006 Loenen W. A. S-Adenosylmethionine: jack of all trades and master of everything? Biochem Soc Trans
2007 Coppins, R. L., Hall, K. B., & Groisman, E. A. The intricate world of riboswitches. Curr Opin Microbiol
2007 Miranda-Ríos J. The THI-box riboswitch, or how RNA binds thiamin pyrophosphate. Structure
2007 Edwards, T. E., Klein, D. J., & Ferré-D'Amaré, A. R. Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr Opin Struct Biol
2008 Wang, J. X. & Breaker, R. R. Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem
2008 Kim, J. N. & Breaker, R. R. Purine sensing by riboswitches. Biol. Cell
2008 Henkin T. M. Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev
2008 Montange, R. K., & Batey, R. T. Riboswitches: emerging themes in RNA structure and function. Annu Rev Biophys
2008 Cochrane, J. C., & Strobel, S. A. Riboswitch effectors as protein enzyme cofactors. RNA
2008 Suess, B., & Weigand, J. E. Engineered riboswitches: overview, problems and trends. RNA Biol
2008 Bocobza, S. E., & Aharoni, A. Switching the light on plant riboswitches. rends Plant Sci
2009 Roth, A. & Breaker, R. R. The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem.
2009 Garst, A. D., & Batey, R. T. A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta
2009 Serganov A. The long and the short of riboswitches. Curr Opin Struct Biol
2009 Blouin, S., Mulhbacher, J., Penedo, J. C., & Lafontaine, D. A. Riboswitches: ancient and promising genetic regulators. Chembiochem
2009 Serganov, A., & Patel, D. J. Amino acid recognition and gene regulation by riboswitches. Biochim Biophys Acta
2010 Wachter A. Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol
2010 Baird, N. J., Kulshina, N., & Ferré-D'Amaré, A. R. Riboswitch function: flipping the switch or tuning the dimmer? RNA Biol
2010 Smith, A. M., Fuchs, R. T., Grundy, F. J., & Henkin, T. M Riboswitch RNAs: regulation of gene expression by direct monitoring of a physiological signal. RNA Biol
2010 Serganov A. Determination of riboswitch structures: light at the end of the tunnel? RNA Biol
2010 Topp, S., & Gallivan, J. P. Emerging applications of riboswitches in chemical biology. ACS Chem Biol
2011 Breaker, R. R. Prospects for riboswitch discovery and analysis. Mol. Cell
2011 Bastet, L., Dubé, A., Massé, E., & Lafontaine, D. A. New insights into riboswitch regulation mechanisms. Mol Microbiol
2011 Haller, A., Soulière, M. F., & Micura, R. The dynamic nature of RNA as key to understanding riboswitch mechanisms. Acc Chem Res
2011 Garst, A. D., Edwards, A. L., & Batey, R. T. Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol
2011 Deigan, K. E., & Ferré-D'Amaré, A. R. Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res
2012 Breaker, R. R. Riboswitches and the RNA world. Cold Spring Harb
2012 Serganov, A., & Patel, D. J. Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annu Rev Biophys
2012 Liberman, J. A., & Wedekind, J. E. Riboswitch structure in the ligand‐free state. Wiley Interdiscip Rev RNA
2012 Serganov, A., & Patel, D. J. Molecular recognition and function of riboswitches. Curr Opin Struct Biol
2013 Serganov, A., & Nudler, E. A decade of riboswitches. Cell
2013 Penchovsky, R., & Stoilova, C. C. Riboswitch-based antibacterial drug discovery using high-throughput screening methods. Expert Opin Drug Discov
2014 Zhang, J., Jones, C. P., & Ferré-D'Amaré, A. R. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim Biophys Acta
2014 Peselis, A., & Serganov, A. Themes and variations in riboswitch structure and function. Biochim Biophys Acta
2014 Savinov, A., Perez, C. F., & Block, S. M. Single-molecule studies of riboswitch folding. Biochim Biophys Acta
2014 Henkin T. M. The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand. Biochim Biophys Acta
2014 Bocobza, S. E., & Aharoni, A. Small molecules that interact with RNA: riboswitch‐based gene control and its involvement in metabolic regulation in plants and algae. Plant J
2014 Porter, E. B., Marcano-Velázquez, J. G., & Batey, R. T. The purine riboswitch as a model system for exploring RNA biology and chemistry. Biochim Biophys Acta
2014 Biochim Biophys Acta. 2014 Oct;1839(10):1005-1019 Fluorescence tools to investigate riboswitch structural dynamics. Biochim Biophys Acta
2014 Soukup, J. K., & Soukup, G. A. Riboswitches exert genetic control through metabolite-induced conformational change. Curr Opin Struct Biol
2015 Peselis, A., Gao, A., & Serganov, A. Cooperativity, allostery and synergism in ligand binding to riboswitches. Biochimie
2015 Berens, C., & Suess, B. Riboswitch engineering—making the all-important second and third steps. Curr Opin Biotechnol
2015 Mellin, J. R., & Cossart, P. Unexpected versatility in bacterial riboswitches. Trends Genet
2015 Fürtig, B., Nozinovic, S., Reining, A., & Schwalbe, H. Multiple conformational states of riboswitches fine-tune gene regulation. Curr Opin Struct Biol
2016 Sherwood, A. V., & Henkin, T. M. Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responses. Annu Rev Microbiol
2017 Jones, C. P., & Ferré-D'Amaré, A. R. Long-range interactions in riboswitch control of gene expression. Annu Rev Biophys
2017 Hallberg, Z. F., Su, Y., Kitto, R. Z., & Hammond, M. C. Engineering and in vivo applications of riboswitches. Annu Rev Biochem
2018 Kreuzer, K. D., & Henkin, T. M. The T-box riboswitch: tRNA as an effector to modulate gene regulation. Microbiol Spectr
2018 Breaker, R. R. Riboswitches and Translation Control. Cold Spring Harb. Perspect. Biol
2018 Lotz, T. S., & Suess, B. Small-Molecule-Binding Riboswitches. Microbiol Spectr
2019 Pavlova, N., Kaloudas, D., & Penchovsky, R. Riboswitch distribution, structure, and function in bacteria. Gene
2019 Pavlova, N., & Penchovsky, R. Genome-wide bioinformatics analysis of FMN, SAM-I, glmS, TPP, lysine, purine, cobalamin, and SAH riboswitches for their applications as allosteric antibacterial drug targets in human pathogenic bacteria. Expert Opin Ther Targets
2019 Yokobayashi Y. Aptamer-based and aptazyme-based riboswitches in mammalian cells. Curr Opin Chem Biol
2019 Arnvig K. B. Riboswitches: choosing the best platform. Biochem Soc Trans
2020 Sherlock, M. E. & Breaker, R. R. Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes. RNA
2020 Bédard, A. V., Hien, E. D. M., & Lafontaine, D. A. Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins. Biochim Biophys Acta Gene Regul Mech
2021 Panchal, V., & Brenk, R. Riboswitches as drug targets for antibiotics. Antibiotics
2022 Hoetzel, J., & Suess, B. Structural changes in aptamers are essential for synthetic riboswitch engineering. J Mol Biol
2022 Vikram, Mishra, V., Rana, A., & Ahire, J. J. Riboswitch-mediated regulation of riboflavin biosynthesis genes in prokaryotes. 3 Biotech
2022 Giarimoglou, N., Kouvela, A., Maniatis, A., Papakyriakou, A., Zhang, J., Stamatopoulou, V., & Stathopoulos, C. A riboswitch-driven era of new antibacterials. Antibiotics
2023 Kavita, K. & Breaker, R. R. Discovering riboswitches: the past and the future. Trends Biochem
2023 Wakchaure, P. D., & Ganguly, B. Exploring the structure, function of thiamine pyrophosphate riboswitch, and designing small molecules for antibacterial activity. Wiley Interdiscip Rev RNA

Articles

Year Riboswitch name Author Title Journal
1988 2'-dG Reichard, P.
 Interactions between deoxyribonucleotide and DNA synthesis. Annu. Rev. Biochem
1992 T-box Henkin, T. M., Glass, B. L. & Grundy, F. J.
 Analysis of the Bacillus subtilis tyrS gene: conservation of a regulatory sequence in multiple tRNA synthetase genes. J. Bacteriol
1993 T-box Grundy, F. J. & Henkin, T. M.
 tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell
1997 Adenine Christiansen, L. C., Schou, S., Nygaard, P. & Saxild, H. H.
 Xanthine metabolism in Bacillus subtilis: characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism. J. Bacteriol
1997 Guanine Christiansen, L. C., Schou, S., Nygaard, P. & Saxild, H. H.
 Xanthine metabolism in Bacillus subtilis: characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism. J. Bacteriol
1998 SAM-I_clan Grundy, F. J. & Henkin, T. M.
 The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol. Microbiol
1999 FMN Gelfand, M. S., Mironov, A. A., Jomantas, J., Kozlov, Y. I. & Perumov, D. A.
 A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet
1999 TPP Begley, T. P. et al.
 Thiamin biosynthesis in prokaryotes. Arch. Microbiol
1999 HMP-PP Begley, T. P. et al.
 Thiamin biosynthesis in prokaryotes. Arch. Microbiol
2000 Cobalamine Nou, X. & Kadner, R. J.
 Adenosylcobalamin inhibits ribosome binding to btuB RNA. Proc. Natl. Acad. Sci. U. S. A
2001 TPP Miranda-Ríos, J., Navarro, M. & Soberón, M.
 A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl. Acad. Sci. U. S. A
2002 FMN Vitreschak, A. G., Rodionov, D. A., Mironov, A. A. & Gelfand, M. S.
 Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res
2002 FMN Winkler, W. C., Cohen-Chalamish, S. & Breaker, R. R.
 An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. U. S. A
2002 TPP Winkler, W., Nahvi, A. & Breaker, R. R.
 Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature
2002 Cobalamine Nahvi, A. et al.
 Genetic control by a metabolite binding mRNA. Chem. Biol
2003 Lysine Grundy, F. J., Lehman, S. C. & Henkin, T. M.
 The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes Proc. Natl. Acad. Sci. U. S. A
2003 Lysine Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S. & Breaker, R. R.
 An mRNA structure in bacteria that controls gene expression by binding lysine Genes Dev
2003 Adenine Johansen, L. E., Nygaard, P., Lassen, C., Agersø, Y. & Saxild, H. H.
 Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL). J. Bacteriol
2003 Guanine Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C. & Breaker, R. R.
 Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria. Cell
2003 TPP Sudarsan, N., Barrick, J. E. & Breaker, R. R.
 Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA
2003 SAM-I_clan Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E., & Breaker, R. R
 An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol
2003 SAM-I_clan McDaniel, B. A., Grundy, F. J., Artsimovitch, I., & Henkin, T. M.
 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 Cobalamine Vitreschak, A. G., Rodionov, D. A., Mironov, A. A. & Gelfand, M. S.
 Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA
2003 Cobalamine Rodionov, D. A., Vitreschak, A. G., Mironov, A. A. & Gelfand, M. S.
 Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J. Biol. Chem
2003 TPP Kubodera, T., M. Watanabe, K. Yoshiuchi, N. Yamashita, A. Nishimura, S. Nakai, K. Gomi and H. Hanamoto.
 Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5'-UTR FEBS Lett
2004 Adenine Mandal, M. & Breaker, R. R.
 Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol
2004 Adenine Serganov, A. et al.
 Structural Basis for Discriminative Regulation of Gene Expression by Adenine- and Guanine-Sensing mRNAs. Chem. Biol
2004 Guanine Serganov, A. et al.
 Structural Basis for Discriminative Regulation of Gene Expression by Adenine- and Guanine-Sensing mRNAs. Chem. Biol
2004 ppGpp Barrick, J. E. et al.
 New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A
2004 PRPP Barrick, J. E. et al.
 New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A
2004 ADP Barrick, J. E. et al.
 New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A
2004 c-di-AMP Barrick, J. E. et al.
 New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A
2004 Magnesium Barrick, J. E. et al.
 New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A
2004 Manganese Barrick, J. E. et al.
 New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A
2004 Guanine Batey, R. T., Gilbert, S. D. & Montange, R. K.
 Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature
2004 GlcN6P Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A. & Breaker, R. R.
 Control of gene expression by a natural metabolite-responsive ribozyme. Nature
2004 GlcN6P Knudsen, S. M. & Ellington, A. D.
 Ribozyme déjà vu. Nat. Struct. Mol. Biol
2004 Glycine Mandal, M. et al.
 A glycine-dependent riboswitch that uses cooperative binding to control gene expression Science
2004 Cobalamine Nahvi, A., Barrick, J. E. & Breaker, R. R.
 Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res
2005 T-box Yousef, M. R., Grundy, F. J. & Henkin, T. M.
 Structural transitions induced by the interaction between tRNA(Gly) and the Bacillus subtilis glyQS T box leader RNA. J. Mol. Biol
2005 FMN Wickiser, J. K., Winkler, W. C., Breaker, R. R. & Crothers, D. M.
 The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol
2005 Adenine Wickiser, J. K., Cheah, M. T., Breaker, R. R. & Crothers, D. M.
 The Kinetics of Ligand Binding by an Adenine-Sensing Riboswitch. Biochemistry
2005 MoCo Schwarz, G.
 Molybdenum cofactor biosynthesis and deficiency. Cell. Mol. Life Sci
2005 Wco Schwarz, G.
 Molybdenum cofactor biosynthesis and deficiency. Cell. Mol. Life Sci
2005 TPP Yamauchi, T. et al.
 Roles of Mg2+ in TPP-dependent riboswitch. FEBS Lett
2005 TPP Sudarsan, N., Cohen-Chalamish, S., Nakamura, S., Emilsson, G. M. & Breaker, R. R.
 Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem. Biol
2005 SAM-II_clan Corbino, K. A., Barrick, J. E., Lim, J., Welz, R., Tucker, B. J., Puskarz, I., Mandal, M., Rudnick, N. D., & Breaker, R. R.
 Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol
2006 Adenine Lemay, J. F., Penedo, J. C., Tremblay, R., Lilley, D. M. & Lafontaine, D. A.
 Folding of the Adenine Riboswitch. Chem. Biol
2006 Guanine Gilbert, S. D., Stoddard, C. D., Wise, S. J. & Batey, R. T.
 Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain. J. Mol. Biol
2006 Magnesium Cromie, M. J., Shi, Y., Latifi, T. & Groisman, E. A.
 An RNA sensor for intracellular Mg(2+). Cell
2006 GlcN6P Jansen, J. A., McCarthy, T. J., Soukup, G. A. & Soukup, J. K.
 Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozyme. Nat. Struct. Mol. Biol
2006 GlcN6P Klein, D. J. & Ferré-D’Amaré, A. R.
 Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science
2006 GlcN6P Soukup, G. A.
 Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure. Nucleic Acids Res
2006 TPP Thore, S., Leibundgut, M. & Ban, N.
 Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science
2006 TPP Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R. & Patel, D. J.
 Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature
2006 TPP Edwards, T. E. & Ferré-D’Amaré, A. R.
 Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule. Recognition Structure
2006 SAM-I_clan Montange, R. K., & Batey, R. T.
 Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature
2006 SAM-II_clan Lim, J., Winkler, W. C., Nakamura, S., Scott, V., & Breaker, R. R.
 Molecular-recognition characteristics of SAM-binding riboswitches. Angew. Chem. Int. Ed Engl
2006 SAM-III Fuchs, R. T., Grundy, F. J., & Henkin, T. M.
 The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat. Struct. Mol. Biol
2006 GlcN6P Roth, A., Nahvi, A., Lee, M., Jona, I. & Breaker, R. R.
 Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA
2007 Lysine Blouin, S. & Lafontaine, D. A.
 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 Lysine Blount, K. F., Wang, J. X., Lim, J., Sudarsan, N. & Breaker, R. R.
 Antibacterial lysine analogs that target lysine riboswitches Nat. Chem. Biol
2007 MoCo Weinberg, Z. et al.
 Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res
2007 Wco Weinberg, Z. et al.
 Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res
2007 SAM-I_clan Weinberg, Z. et al.
 Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res
2007 c-AMP-GMP Weinberg, Z. et al.
 Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res
2007 c-di-GMP Weinberg, Z. et al.
 Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res
2007 2'-dG Kim, J. N., Roth, A. & Breaker, R. R.
 Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Proc. Natl. Acad. Sci. U. S. A
2007 Magnesium Dann, C. E., 3rd et al.
 Structure and mechanism of a metal-sensing regulatory RNA. Cell
2007 TPP Bocobza, S. et al.
 Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev
2007 TPP Cheah, M. T., Wachter, A., Sudarsan, N. & Breaker, R. R.
 Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature
2007 TPP Wachter, A. et al.
 Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell
2007 Glycine Lipfert, J. et al.
 Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae J. Mol. Biol
2007 SAM-I_clan Yao, Z., Barrick, J., Weinberg, Z., Neph, S., Breaker, R., Tompa, M., and Ruzzo, W.L.
 A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput. Biol
2007 PreQ1 Roth, A. et al
 A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain Nat. Struct. Mol. Biol
2007 SAM-III Fuchs, R. T., Grundy, F. J., & Henkin, T. M.
 S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the S(MK) box translational riboswitch RNA. Proc. Natl. Acad. Sci. U. S. A
2008 Lysine Garst, A. D., Héroux, A., Rambo, R. P. & Batey, R. T.
 Crystal structure of the lysine riboswitch regulatory mRNA element J. Biol. Chem
2008 Lysine Serganov, A., Huang, L. & Patel, D. J.
 Structural insights into amino acid binding and gene control by a lysine riboswitch Nature
2008 SAH Wang, J. X., Lee, E. R., Morales, D. R., Lim, J., & Breaker, R. R.
 Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol
2008 MoCo Regulski, E. E. et al.
 A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol. Microbiol
2008 Wco Regulski, E. E. et al.
 A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol. Microbiol
2008 MoCo Bevers, L. E. et al.
 Function of MoaB proteins in the biosynthesis of the molybdenum and tungsten cofactors. Biochemistry
2008 Wco Bevers, L. E. et al.
 Function of MoaB proteins in the biosynthesis of the molybdenum and tungsten cofactors. Biochemistry
2008 TPP Thore, S., Frick, C. & Ban, N.
 Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch. J. Am. Chem. Soc
2008 Glycine Kwon, M. & Strobel, S. A.
 Chemical basis of glycine riboswitch cooperativity RNA
2008 SAM-I_clan Weinberg, Z., Regulski, E. E., Hammond, M. C., Barrick, J. E., Yao, Z., Ruzzo, W. L., & Breaker, R. R.
 The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA
2008 SAM-II_clan Gilbert, S. D., Rambo, R. P., Van Tyne, D., & Batey, R. T.
 Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat. Struct. Mol. Biol
2008 PreQ1 Meyer, M. M., Roth, A., Chervin, S. M., Garcia, G. A. & Breaker, R. R
 Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria RNA
2008 SAM-III Lu, C., Smith, A. M., Fuchs, R. T., Ding, F., Rajashankar, K., Henkin, T. M., & Ke, A.
 Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat. Struct. Mol. Biol
2008 c-di-GMP Sudarsan, N. et al.
 Riboswitches in eubacteria sense the second messenger cyclic di-GMP Science
2009 T-box Gutiérrez-Preciado, A., Henkin, T. M., Grundy, F. J., Yanofsky, C. & Merino, E.
 Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol. Mol. Biol. Rev
2009 FMN Lee, E. R., Blount, K. F. & Breaker, R. R.
 Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol
2009 FMN Serganov, A., Huang, L. & Patel, D. J.
 Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature
2009 Guanine Gilbert, S. D., Reyes, F. E., Edwards, A. L. & Batey, R. T.
 Adaptive Ligand Binding by the Purine Riboswitch in the Recognition of Guanine and Adenine Analogs. Structure
2009 Magnesium Wakeman, C. A., Ramesh, A. & Winkler, W. C.
 Multiple metal-binding cores are required for metalloregulation by M-box riboswitch RNAs. J. Mol. Biol
2009 GlcN6P Cochrane, J. C., Lipchock, S. V., Smith, K. D. & Strobel, S. A.
 Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme. Biochemistry
2009 SAM-II_clan Meyer, M. M., Ames, T. D., Smith, D. P., Weinberg, Z., Schwalbach, M. S., Giovannoni, S. J., & Breaker, R. R.
 Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter Ubique'. BMC Genomics
2009 SAM-II_clan Poiata, E., Meyer, M. M., Ames, T. D., & Breaker, R. R.
 A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA
2009 PreQ1 Klein, D. J., Edwards, T. E. & Ferré-D’Amaré, A. R.
 Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat. Struct. Mol. Biol
2009 PreQ1 Kang, M., Peterson, R. & Feigon, J.
 Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of Trna. Mol. Cell
2009 PreQ1 Spitale, R. C., Torelli, A. T., Krucinska, J., Bandarian, V. & Wedekind, J. E.
 The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain. J. Biol. Chem
2009 c-di-GMP Smith, K. D. et al
 Structural basis of ligand binding by a c-di-GMP riboswitch Nat. Struct. Mol. Biol
2010 Adenine Delfosse, V. et al.
 Riboswitch structure: an internal residue mimicking the purine ligand. Nucleic Acids Res
2010 SAH Edwards, A. L., Reyes, F. E., Héroux, A., & Batey, R. T.
 Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA
2010 SAH Chou, M. Y., Lin, S. C., & Chang, K. Y.
 Stimulation of -1 programmed ribosomal frameshifting by a metabolite-responsive RNA pseudoknot. RNA
2010 Cobalamine Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R.
 Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol
2010 SAM-I_clan Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R.
 Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol
2010 SAM-SAH Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R.
 Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol
2010 ZTP Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R.
 Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol
2010 Fluoride Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R.
 Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol
2010 TPP Kulshina, N., Edwards, T. E. & Ferré-D’Amaré, A. R.
 Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate. riboswitch RNA
2010 Glycine Huang, L., Serganov, A. & Patel, D. J.
 Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch Mol. Cell
2010 Glycine Lipfert, J., Sim, A. Y. L., Herschlag, D. & Doniach, S.
 Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding RNA
2010 SAM-I_clan Montange, R. K., Mondragón, E., van Tyne, D., Garst, A. D., Ceres, P., & Batey, R. T.
 Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J. Mol. Biol
2010 SAM-I_clan Stoddard, C. D., Montange, R. K., Hennelly, S. P., Rambo, R. P., Sanbonmatsu, K. Y., & Batey, R. T.
 Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure
2010 SAM-I_clan Lu, C., Ding, F., Chowdhury, A., Pradhan, V., Tomsic, J., Holmes, W. M., Henkin, T. M., & Ke, A.
 SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch. J. Mol. Biol
2010 THF Ames, T. D., Rodionov, D. A., Weinberg, Z. & Breaker, R. R.
 A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem. Biol
2010 PreQ1 Rieder, U., Kreutz, C. & Micura, R.
 Folding of a transcriptionally acting preQ1 riboswitch. Proc. Natl. Acad. Sci. U. S. A
2010 SAM-III Priyakumar U. D.
 Atomistic details of the ligand discrimination mechanism of S(MK)/SAM-III riboswitch. J. Phys. Chem
2010 SAM-III Smith, A. M., Fuchs, R. T., Grundy, F. J., & Henkin, T. M.
 The SAM-responsive S(MK) box is a reversible riboswitch. Mol. Microbiol
2010 c-di-GMP Smith, K. D., Lipchock, S. V., Livingston, A. L., Shanahan, C. A. & Strobel, S. A.
 Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch Biochemistry
2010 c-di-GMP Lee, E. R., Baker, J. L., Weinberg, Z., Sudarsan, N. & Breaker, R. R.
 An allosteric self-splicing ribozyme triggered by a bacterial second messenger Science
2011 Glutamine Ames, T. D. & Breaker, R. R.
 Bacterial aptamers that selectively bind glutamine RNA Biol
2011 Lysine Blouin, S., Chinnappan, R. & Lafontaine, D. A.
 Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation Nucleic Acids Res
2011 FMN Vicens, Q., Mondragón, E. & Batey, R. T.
 Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection. Nucleic Acids Res
2011 2'-dG Pikovskaya, O., Polonskaia, A., Patel, D. J. & Serganov, A.
 Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch. Nat. Chem. Biol
2011 Guanine Buck, J. et al.
 Influence of ground-state structure and Mg 2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res
2011 Magnesium Ramesh, A., Wakeman, C. A. & Winkler, W. C.
 Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. J. Mol. Biol
2011 GlcN6P Watson, P. Y. & Fedor, M. J.
 The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. Nat. Struct. Mol. Biol
2011 Glycine Butler, E. B., Xiong, Y., Wang, J. & Strobel, S. A.
 Structural basis of cooperative ligand binding by the glycine riboswitch Chem. Biol
2011 Glycine Erion, T. V. & Strobel, S. A.
 Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch RNA
2011 SAM-I_clan Heppell, B., Blouin, S., Dussault, A. M., Mulhbacher, J., Ennifar, E., Penedo, J. C., & Lafontaine, D. A.
 Molecular insights into the ligand-controlled organization of the SAM-I riboswitch. Nat. Chem. Biol
2011 THF Huang, L., Ishibe-Murakami, S., Patel, D. J. & Serganov, A.
 Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch. Proc. Natl. Acad. Sci. U. S. A
2011 THF Trausch, J. J., Ceres, P., Reyes, F. E. & Batey, R. T.
 The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure
2011 SAM-II_clan Haller, A., Rieder, U., Aigner, M., Blanchard, S. C., & Micura, R.
 Conformational capture of the SAM-II riboswitch. Nat. Chem. Biol
2011 PreQ1 Jenkins, J. L., Krucinska, J., McCarty, R. M., Bandarian, V. & Wedekind, J. E.
 Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation. J. Biol. Chem
2011 SAM-III Lu, C., Smith, A. M., Ding, F., Chowdhury, A., Henkin, T. M., & Ke, A.
 Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. J. Mol. Biol
2011 c-di-GMP Smith, K. D., Shanahan, C. A., Moore, E. L., Simon, A. C. & Strobel, S. A.
 Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches Proc. Natl. Acad. Sci. U. S. A
2012 Lysine Garst, A. D., Porter, E. B. & Batey, R. T.
 Insights into the regulatory landscape of the lysine riboswitch J. Mol. Biol
2012 Lysine Budhathoki, P., Bernal-Perez, L. F., Annunziata, O. & Ryu, Y.
 Rationally-designed fluorescent lysine riboswitch probes Org. Biomol. Chem
2012 Lysine Wilson-Mitchell, S. N., Grundy, F. J. & Henkin, T. M.
 Analysis of lysine recognition and specificity of the Bacillus subtilis L box riboswitch Nucleic Acids Res
2012 Adenine Frieda, K. L. & Block, S. M.
 Direct observation of cotranscriptional folding in an adenine riboswitch. Science
2012 GlcN6P Viladoms, J. & Fedor, M. J.
 The glmS ribozyme cofactor is a general acid-base catalyst. J. Am. Chem. Soc
2012 SAM-I_clan Eschbach, S. H., St-Pierre, P., Penedo, J. C., & Lafontaine, D. A.
 Folding of the SAM-I riboswitch: a tale with a twist. RNA Biol
2012 SAM-I_clan Boyapati, V. K., Huang, W., Spedale, J., & Aboul-Ela, F.
 Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch. RNA
2012 c-di-AMP Watson, P. Y. & Fedor, M. J.
 The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis. Nat. Chem. Biol
2012 Cobalamine Johnson, J. E., Reyes, F. E., Polaski, J. T. & Batey, R. T.
 B12 cofactors directly stabilize an mRNA regulatory switch. Nature
2012 Cobalamine Peselis, A. & Serganov, A.
 Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch. Nat. Struct. Mol. Biol
2012 SAM-II_clan Chen, B., Zuo, X., Wang, Y. X., & Dayie, T. K.
 Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy. Nucleic Acids Res
2012 SAM-II_clan Doshi, U., Kelley, J. M., & Hamelberg, D.
 Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch. RNA
2012 PreQ1 Santner, T., Rieder, U., Kreutz, C. & Micura, R.
 Pseudoknot preorganization of the preQ1 class I riboswitch. J. Am. Chem. Soc
2012 Fluoride Baker, J. L. et al.
 Widespread genetic switches and toxicity resistance proteins for fluoride. Science
2012 Fluoride Ren, A., Rajashankar, K. R. & Patel, D. J.
 Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature
2012 c-di-GMP Smith, K. D., Lipchock, S. V. & Strobel, S. A.
 Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer Biochemistry
2013 T-box Zhang, J. & Ferré-D’Amaré, A. R.
 Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature
2013 MoCo Iobbi-Nivol, C. & Leimkühler, .
 Molybdenum enzymes, their maturation and molybdenum cofactor biosynthesis in Escherichia coli. Biochim. Biophys
2013 Wco Iobbi-Nivol, C. & Leimkühler, .
 Molybdenum enzymes, their maturation and molybdenum cofactor biosynthesis in Escherichia coli. Biochim. Biophys
2013 c-di-AMP Nelson, J. W. et al.
 Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat. Chem. Biol
2013 PreQ1 Soulière, M. F. et al.
 Tuning a riboswitch response through structural extension of a pseudoknot. Proc. Natl. Acad. Sci. U. S. A
2013 PreQ1 Liberman, J. A., Salim, M., Krucinska, J. & Wedekind, J. E.
 Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat. Chem. Biol
2013 c-di-GMP Kalia, D. et al.
 Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis Chem. Soc. Rev
2014 SAM-I_clan Price IR, Grigg JC, Ke A.
 Common themes and differences in SAM recognition among SAM riboswitches. Biochim Biophys Acta
2014 SAM-II_clan Price IR, Grigg JC, Ke A.
 Common themes and differences in SAM recognition among SAM riboswitches. Biochim Biophys Acta
2014 SAM-III Price IR, Grigg JC, Ke A.
 Common themes and differences in SAM recognition among SAM riboswitches. Biochim Biophys Acta
2014 TPP Warner, K. D. et al.
 Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol
2014 Glycine Ruff, K. M. & Strobel, S. A.
 Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy RNA
2014 SAM-I_clan Trausch, J. J., Xu, Z., Edwards, A. L., Reyes, F. E., Ross, P. E., Knight, R., & Batey, R. T.
 Structural basis for diversity in the SAM clan of riboswitches. Proc. Natl. Acad. Sci. U. S. A
2014 THF Trausch, J. J. & Batey, R. T.
 A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch. Chem. Biol
2014 c-di-AMP Ren, A. & Patel, D. J.
 c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Nat. Chem. Biol
2014 c-di-AMP Gao, A. & Serganov, A.
 Structural insights into recognition of c-di-AMP by the ydaO riboswitch. Nat. Chem. Biol
2014 c-di-AMP Jones, C. P. & Ferré-D’Amaré, A. R.
 Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. EMBO J
2014 Cobalamine Choudhary, P. K. & Sigel, R. K.
 Mg2+-induced conformational changes in the btuB riboswitch from E. coli. RNA
2014 PreQ1 Kang, M., Eichhorn, C. D. & Feigon, J.
 Structural determinants for ligand capture by a class II preQ1 riboswitch. Proc. Natl. Acad. Sci. U. S. A
2014 PreQ1 McCown, P. J., Liang, J. J., Weinberg, Z. & Breaker, R. R.
 Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes. Chem. Biol
2015 Glutamine Ren, A. et al.
 Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch Cell Rep
2015 Lysine Zhou, L.-B. & Zeng, A.-P.
 Engineering a Lysine-ON Riboswitch for Metabolic Control of Lysine Production in Corynebacterium glutamicum ACS Synth. Biol
2015 Lysine Zhou, L.-B. & Zeng, A.-P.
 Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum ACS Synth. Biol
2015 Lysine Smith-Peter, E., Lamontagne, A.-M. & Lafontaine, D. A.
 Role of lysine binding residues in the global folding of the lysC riboswitch RNA Biol
2015 T-box Sherwood, A. V., Grundy, F. J. & Henkin, T. M.
 T box riboswitches in Actinobacteria: translational regulation via novel tRNA interactions. Proc. Natl. Acad. Sci. U. S. A
2015 FMN Blount, K. F. et al.
 Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob. Agents Chemother
2015 FMN Howe, J. A. et al.
 Selective small-molecule inhibition of an RNA structural element. Nature
2015 NiCo Furukawa, K. et al.
 Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Mol. Cell
2015 c-AMP-GMP Nelson, J. W. et al.
 Control of bacterial exoelectrogenesis by c-AMP-GMP. Proc. Natl. Acad. Sci. U. S. A
2015 c-AMP-GMP Ren, A. et al.
 Structural basis for molecular discrimination by a 3',3'-cGAMP sensing riboswitch. Cell Rep
2015 c-AMP-GMP Kellenberger, C. A. et al.
 GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP. Proc. Natl. Acad. Sci. U. S. A
2015 ZTP Kim, P. B., Nelson, J. W. & Breaker, R. R.
 An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism Mol. Cell
2015 ZTP Ren, A., Rajashankar, K. R. & Patel, D. J.
 Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism Structure
2015 ZTP Trausch, J. J., Marcano-Velázquez, J. G., Matyjasik, M. M. & Batey, R. T.
 Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch Chem. Biol
2015 ZTP Jones, C. P. & Ferré-D’Amaré, A. R.
 Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains Nat. Struct. Mol. Biol
2015 Guanine Hernandez, A. R. et al.
 A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair. Angew. Chem. Int. Ed Engl
2015 MoCo Hover, B. M., Tonthat, N. K., Schumacher, M. A. & Yokoyama, K.
 Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. U. S. A
2015 Wco Hover, B. M., Tonthat, N. K., Schumacher, M. A. & Yokoyama, K.
 Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. U. S. A
2015 TPP Yadav, S., Swati, D. & Chandrasekharan, H.
 Thiamine pyrophosphate riboswitch in some representative plant species: a bioinformatics study. J. Comput. Biol
2015 Manganese Dambach, M. et al.
 The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol. Cell
2015 Manganese Price, I. R., Gaballa, A., Ding, F., Helmann, J. D. & Ke, A.
 Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol. Cell
2015 SAM-II_clan Xue, X., Yongjun, W., & Zhihong, L.
 Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation. J. Theor. Biol
2015 PreQ1 Liberman, J. A.
 Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc. Natl. Acad. Sci. U. S. A
2015 Fluoride Chawla, M., Credendino, R., Poater, A., Oliva, R. & Cavallo, L.
 Structural stability, acidity, and halide selectivity of the fluoride riboswitch recognition site. J. Am. Chem. Soc
2015 c-di-GMP Bordeleau, E. et al.
 Cyclic di-GMP riboswitch-regulated type IV pili contribute to aggregation of Clostridium difficile J. Bacteriol
2016 FMN Howe, J. A., L. Xiao, T. O. Fischmann, H. Wang, H. Tang, A. Villafania, R. Zhang, C. M. Barbieri and T. Roemer.
 Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch. RNA Biol
2016 Azaaromatic Li, S., Hwang, X. Y., Stav, S. & Breaker, R. R.
 The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA
2016 Glycine Ketterer, S., Gladis, L., Kozica, A. & Meier, M.
 Engineering and characterization of fluorogenic glycine riboswitches Nucleic Acids Res
2016 Glycine Ruff, K. M., Muhammad, A., McCown, P. J., Breaker, R. R. & Strobel, S. A.
 Singlet glycine riboswitches bind ligand as well as tandem riboswitches RNA
2016 SAM-II_clan Chen, B., LeBlanc, R., & Dayie, T. K.
 SAM-II riboswitch samples at least two conformations in solution in the absence of ligand: implications for recognition. Angew. Chem. Int. Ed Engl
2016 SAM-III Suresh, G., Srinivasan, H., Nanda, S., & Priyakumar, U. D.
 Ligand-induced stabilization of a duplex-like architecture is crucial for the switching mechanism of the SAM-III riboswitch. Biochemistry
2016 SAM-III Gong, S., Wang, Y., Wang, Z., Wang, Y., & Zhang, W.
 Reversible-switch mechanism of the SAM-III riboswitch. J. Phys. Chem
2017 Lysine Mukherjee, S., Barash, D. & Sengupta, S.
 Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria PLoS One
2017 FMN Weinberg, Z., Nelson, J. W., Lünse, C. E., Sherlock, M. E. & Breaker, R. R.
 Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proc. Natl. Acad. Sci. U. S. A
2017 2'-dG Weinberg, Z., Nelson, J. W., Lünse, C. E., Sherlock, M. E. & Breaker, R. R.
 Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proc. Natl. Acad. Sci. U. S. A
2017 Adenine Stagno, J. R. et al.
 Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature
2017 THF Weinberg, Z., Lünse, C. E., Corbino, K. A., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K. R., Sherlock, M. E., & Breaker, R. R.
 Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res
2017 NAD+-I Weinberg, Z., Lünse, C. E., Corbino, K. A., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K. R., Sherlock, M. E., & Breaker, R. R.
 Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res
2017 SAM-SAH Weinberg, Z., Lünse, C. E., Corbino, K. A., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K. R., Sherlock, M. E., & Breaker, R. R.
 Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res
2017 PRA Weinberg, Z., Lünse, C. E., Corbino, K. A., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K. R., Sherlock, M. E., & Breaker, R. R.
 Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res
2017 Xanthine Weinberg, Z., Lünse, C. E., Corbino, K. A., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K. R., Sherlock, M. E., & Breaker, R. R.
 Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res
2017 Li+ Weinberg, Z., Lünse, C. E., Corbino, K. A., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K. R., Sherlock, M. E., & Breaker, R. R.
 Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res
2017 Na+ Weinberg, Z., Lünse, C. E., Corbino, K. A., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K. R., Sherlock, M. E., & Breaker, R. R.
 Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res
2017 Guanidine Nelson, J. W., Atilho, R. M., Sherlock, M. E., Stockbridge, R. B. & Breaker, R. R.
 Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Mol. Cell
2017 ADP Nelson, J. W., Atilho, R. M., Sherlock, M. E., Stockbridge, R. B. & Breaker, R. R.
 Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Mol. Cell
2017 PRPP Nelson, J. W., Atilho, R. M., Sherlock, M. E., Stockbridge, R. B. & Breaker, R. R.
 Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Mol. Cell
2017 ppGpp Nelson, J. W., Atilho, R. M., Sherlock, M. E., Stockbridge, R. B. & Breaker, R. R.
 Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Mol. Cell
2017 Guanidine Sherlock, M. E., Malkowski, S. N. & Breaker, R. R.
 Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria. Biochemistry
2017 Guanidine Sherlock, M. E. & Breaker, R. R.
 Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria. Biochemistry
2017 Guanidine Reiss, C. W., Xiong, Y. & Strobel, S. A.
 Structural Basis for Ligand Binding to the Guanidine-I Riboswitch. Structure
2017 Guanidine Battaglia, R. A., Price, I. R. & Ke, A.
 ykkCStructural basis for guanidine sensing by the family of riboswitches. RNA
2017 Guanidine Huang, L., Wang, J. & Lilley, D. M. J.
 The Structure of the Guanidine-II Riboswitch. Cell Chem Biol
2017 Guanidine Reiss, C. W. & Strobel, S. A.
 Structural basis for ligand binding to the guanidine-II riboswitch. RNA
2017 Guanidine Huang, L., Wang, J., Wilson, T. J. & Lilley, D. M. J.
 Structure of the Guanidine III Riboswitch. Cell Chem Biol
2017 GlcN6P Bingaman, J. L. et al.
 The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat. Chem. Biol
2017 Glycine Babina, A. M., Lea, N. E. & Meyer, M. M.
 In Vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis MBio
2017 SAM-I_clan Dussault, A.-M., Dubé, A., Jacques, F., Grondin, J. P., and Lafontaine, D. A.
 Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism. RNA
2017 SAM-I_clan Manz, C., Kobitski, A. Y., Samanta, A., Keller, B. G., Jäschke, A., & Nienhaus, G. U.
 Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat. Chem. Biol
2017 Cobalamine Choudhary, P. K., Gallo, S. & Sigel, R. K.
 Tb(3+)-Cleavage Assays Reveal Specific Mg(2+) Binding Sites Necessary to Pre-fold the btuB Riboswitch for AdoCbl Binding. Frontiers in chemistry
2017 Cobalamine Polaski, J. T., Webster, S. M., Johnson, J. E. & Batey, R. T.
 Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin. J. Biol. Chem
2017 SAM-II_clan Roy, S., Lammert, H., Hayes, R. L., Chen, B., LeBlanc, R., Dayie, T. K., Onuchic, J. N., & Sanbonmatsu, K. Y.
 A magnesium-induced triplex pre-organizes the SAM-II riboswitch. PLoS Comput. Biol
2017 Fluoride Zhao, B., Guffy, S. L., Williams, B. & Zhang, Q.
 An excited state underlies gene regulation of a transcriptional riboswitch. Nat. Chem. Biol
2018 Glutamine Klähn, S. et al.
 A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria Nucleic Acids Res
2018 FMN Rizvi, N. F. et al.
 Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry. ACS Chem. Biol
2018 FMN Vicens, Q. et al.
 Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch. ACS Chem. Biol
2018 c-AMP-GMP Keller, H., Weickhmann, A. K., Bock, T. & Wöhnert, J.
 Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches. RNA
2018 c-AMP-GMP Li, C., Zhao, X., Zhu, X., Xie, P. & Chen, G.
 Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation. Int. J. Mol. Sci
2018 SAM-SAH Weickhmann, A. K., Keller, H., Duchardt-Ferner, E., Strebitzer, E., Juen, M. A., Kremser, J., Wurm, J. P., Kreutz, C., & Wöhnert, J.
 NMR resonance assignments for the SAM/SAH-binding riboswitch RNA bound to S-adenosylhomocysteine. Biomol. NMR Assign
2018 SAM-VI Mirihana Arachchilage, G., Sherlock, M. E., Weinberg, Z., & Breaker, R. R.
 SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches. RNA Biol
2018 ppGpp Sherlock, M. E., Sudarsan, N., Stav, S. & Breaker, R. R.
 Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria. Elife
2018 PRPP Sherlock, M. E., Sudarsan, N., Stav, S. & Breaker, R. R.
 Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria. Elife
2018 ADP Sherlock, M. E., Sudarsan, N., Stav, S. & Breaker, R. R.
 Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria. Elife
2018 ppGpp Sherlock, M. E., Sudarsan, N. & Breaker, R. R.
 Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems. Proc. Natl. Acad. Sci. U. S. A
2018 PRPP Peselis, A. & Serganov, A.
 ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands. Nat. Chem. Biol
2018 ppGpp Peselis, A. & Serganov, A.
 ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands. Nat. Chem. Biol
2018 PRPP Knappenberger, A. J., Reiss, C. W. & Strobel, S. A.
 Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA. Elife
2018 Azaaromatic Gong, S., Wang, Y., Wang, Z., Wang, Y. & Zhang, W.
 Genetic regulation mechanism of the yjdF riboswitch. J. Theor. Biol
2018 TPP Mukherjee, S., Retwitzer, Barash, D. & Sengupta, S.
 Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi. Sci. Rep
2018 Manganese Bachas, S. T. & Ferré-D’Amaré, A. R.
 Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators. Cell Chem Biol 25, 962–973
2018 Glycine Khani, A., Popp, N., Kreikemeyer, B. & Patenge, N.
 A Glycine Riboswitch in Controls Expression of a Sodium:Alanine Symporter Family Protein Gene Front. Microbiol
2018 SAM-I_clan Manz, C., Kobitski, A. Y., Samanta, A., Jäschke, A., & Nienhaus, G. U.
 The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study. J. Chem. Phys
2018 SAM-II_clan Huang, L., & Lilley, D. M. J.
 Structure and ligand binding of the SAM-V riboswitch. Nucleic Acids Res
2018 PreQ1 Widom, J. R. et al.
 Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing. Mol. Cell
2018 c-di-GMP Inuzuka, S. et al.
 Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain Genes Cells
2019 Glutamine Huang, L., Wang, J., Watkins, A. M., Das, R. & Lilley, D. M. J.
 Structure and ligand binding of the glutamine-II riboswitch Nucleic Acids Res
2019 T-box Battaglia, R. A., Grigg, J. C. & Ke, A.
 Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Nat. Struct. Mol. Biol
2019 T-box Li, S. et al.
 Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nat. Struct. Mol. Biol
2019 T-box Weaver, J. W. & Serganov, A.
 T-box RNA gets boxed. Nat. Struct. Mol. Biol
2019 2'-dG Matyjasik, M. M. & Batey, R. T.
 Structural basis for 2′-deoxyguanosine recognition by the 2′-dG-II class of riboswitches. Nucleic Acids Res
2019 SAM-SAH Weickhmann, A. K., Keller, H., Wurm, J. P., Strebitzer, E., Juen, M. A., Kremser, J., Weinberg, Z., Kreutz, C., Duchardt-Ferner, E., & Wöhnert, J.
 The structure of the SAM/SAH-binding riboswitch. Nucleic Acids Res
2019 ZTP Jones, C. et al.
 Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun
2019 ZTP Strobel, E. J., Cheng, L., Berman, K. E., Carlson, P. D. & Lucks, J. B.
 A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control Nat. Chem. Biol
2019 ZTP Perkins, K. R., Atilho, R. M., Moon, M. H. & Breaker, R. R.
 Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-Throughput Screen ACS Chem. Biol
2019 Guanidine Huang, L., Wang, J., Wilson, T. J. & Lilley, D. M. J.
 Structure-guided design of a high-affinity ligand for a riboswitch. RNA
2019 SAM-VI Sun, A., Gasser, C., Li, F., Chen, H., Mair, S., Krasheninina, O., Micura, R., & Ren, A.
 SAM-VI riboswitch structure and signature for ligand discrimination. Nat. Commun
2019 TPP Stav, S. et al.
 Genome-wide discovery of structured noncoding RNAs in bacteria. BMC Microbiol
2019 HMP-PP Stav, S. et al.
 Genome-wide discovery of structured noncoding RNAs in bacteria. BMC Microbiol
2019 Manganese Martin, J. E. et al.
 A Mn-sensing riboswitch activates expression of a Mn2+/Ca2+ ATPase transporter in Streptococcus. Nucleic Acids Res
2019 Manganese Suddala, K. C. et al.
 Local-to-global signal transduction at the core of a Mn sensing riboswitch. Nat. Commun
2019 Glycine Zhou, L. et al.
 Characterization and Engineering of a Clostridium Glycine Riboswitch and Its Use To Control a Novel Metabolic Pathway for 5-Aminolevulinic Acid Production in Escherichia coli ACS Synth. Biol
2019 ADP Sherlock, M. E., Sadeeshkumar, H. & Breaker, R. R.
 Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates. Biochemistry
2019 SAM-I_clan Zhang, K., Li, S., Kappel, K., Pintilie, G., Su, Z., Mou, T. C., Schmid, M. F., Das, R., & Chiu, W.
 Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nat. Commun
2019 THF Chen, X., Mirihana, A. G. & Breaker, R. R.
 Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria. RNA
2019 c-di-AMP Wang, X. et al.
 A c-di-AMP riboswitch controlling kdpFABC operon transcription regulates the potassium transporter system in Bacillus thuringiensis. Commun Biol
2019 NAD+-I Malkowski, S. N., Spencer, T. C. J. & Breaker, R. R.
 Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD RNA
2019 PreQ1 Connelly, C. M. et al.
 Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure. Nat. Commun
2019 HMP-PP Atilho, R. M., Mirihana, A. G., Greenlee, E. B., Knecht, K. M. & Breaker, R. R.
 A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer. Elife
2020 Lysine Sung, H.-L. & Nesbitt, D. J.
 High pressure single-molecule FRET studies of the lysine riboswitch: cationic and osmolytic effects on pressure induced denaturation Phys. Chem. Chem. Phys
2020 FMN Wilt, H. M., Yu, P., Tan, K., Wang, Y. X. & Stagno, J. R.
 FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations. Journal of structural biology
2020 NiCo Xu, J. & Cotruvo, J. A., Jr.
 The (NiCo) Riboswitch Responds to Iron(II). Biochemistry
2020 SAM-SAH Huang, L., Liao, T. W., Wang, J., Ha, T., & Lilley, D. M. J.
 Crystal structure and ligand-induced folding of the SAM/SAH riboswitch. Nucleic Acids Res
2020 ZTP Tran, B. et al.
 Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design Cell Chem Biol
2020 ZTP Hua, B. et al.
 Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape Nat. Commun
2020 Guanidine Wuebben, C., Vicino, M. F., Mueller, M. & Schiemann, O.
 Do the P1 and P2 hairpins of the Guanidine-II riboswitch interact? Nucleic Acids Res
2020 Guanidine Salvail, H., Balaji, A., Yu, D., Roth, A. & Breaker, R. R.
 Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria. Biochemistry
2020 Guanidine Lenkeit, F., Eckert, I., Hartig, J. S. & Weinberg, Z.
 Discovery and characterization of a fourth class of guanidine riboswitches. Nucleic Acids Res
2020 PRA Malkowski, S. N., Atilho, R. M., Greenlee, E. B., Weinberg, C. E. & Breaker, R. R.
 A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine. RNA
2020 Xanthine Yu, D. & Breaker, R. R.
 A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation. RNA
2020 TPP Subki, A., Ho, C. L., Ismail, N. F. N., Aa, Z. A. & Zn, B. Y.
 Identification and characterisation of thiamine pyrophosphate (TPP) riboswitch in Elaeis guineensis. PLoS One
2020 Glycine Kappel, K. et al.
 Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures Nat
2020 Glycine Torgerson, C. D., Hiller, D. A. & Strobel, S. A.
 The asymmetry and cooperativity of tandem glycine riboswitch aptamers RNA
2020 SAM-I_clan Tang, D. J., Du, X., Shi, Q., Zhang, J. L., He, Y. P., Chen, Y. M., Ming, Z., Wang, D., Zhong, W. Y., Liang, Y. W., Liu, J. Y., Huang, J. M., Zhong, Y. S., An, S. Q., Gu, H., & Tang, J. L.
 A SAM-I riboswitch with the ability to sense and respond to uncharged initiator tRNA. Nat. Commun
2020 NAD+-I Huang, L., Wang, J. & Lilley, D. M. J.
 Structure and ligand binding of the ADP-binding domain of the NAD+ riboswitch RNA
2020 NAD+-I Chen, H. et al.
 Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding Nucleic Acids Res
2020 Cobalamine Chan, C. W. & Mondragón, A.
 Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding. Nucleic Acids Res
2020 PreQ1 Schroeder, G. M. et al.
 Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation. Nucleic Acids Res
2021 FMN Harale, B. et al.
 Synthesis and evaluation of antimycobacterial activity of riboflavin derivatives. Bioorg. Med. Chem. Lett
2021 Adenine St-Pierre, P. et al.
 A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition. Nucleic Acids Res
2021 Guanidine Sinn, M., Hauth, F., Lenkeit, F., Weinberg, Z. & Hartig, J. S.
 Widespread bacterial utilization of guanidine as nitrogen source. Mol. Microbiol
2021 ppGpp Sun, Z. et al.
 Live-Cell Imaging of Guanosine Tetra- and Pentaphosphate (p)ppGpp with RNA-based Fluorescent Sensors*. Angew. Chem. Int. Ed Engl
2021 Xanthine Xu, X. et al.
 Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition. Nucleic Acids Res
2021 GlcN6P Traykovska, M., Popova, K. B. & Penchovsky, R.
 Targeting glmS Ribozyme with Chimeric Antisense Oligonucleotides for Antibacterial Drug Development. ACS Synth. Biol
2021 THF Wilt, H. M., Yu, P., Tan, K., Wang, Y. X. & Stagno, J. R.
 Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation. J. Struct. Biol
2021 NAD+-II Brewer, K. I. et al.
 Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes RNA Biol
2021 NAD+-II Panchapakesan, S. S. S., Corey, L., Malkowski, S. N., Higgs, G. & Breaker, R. R.
 A second riboswitch class for the enzyme cofactor NAD RNA
2021 Cobalamine Ma, B., Bai, G., Nussinov, R., Ding, J. & Wang, Y.-X.
 Conformational Ensemble of AdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition. J. Phys. Chem
2021 PreQ1 Flemmich, L., Heel, S., Moreno, S., Breuker, K. & Micura, R.
 A natural riboswitch scaffold with self-methylation activity. Nat. Commun
2021 Fluoride Chauvier, A., Ajmera, P., Yadav, R. & Walter, N. G.
 Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation. Proc. Natl. Acad. Sci. U. S. A
2022 FMN Traykovska, M. & Penchovsky, R.
 Engineering Antisense Oligonucleotides as Antibacterial Agents That Target FMN Riboswitches and Inhibit the Growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli. ACS Synth. Biol
2022 NiCo Xu, J. & Cotruvo, J. A., Jr.
 Iron-responsive riboswitches. Curr. Opin. Chem. Biol
2022 NiCo Xu, J. & Cotruvo, J. A., Jr.
 Reconsidering the (NiCo) Riboswitch as an Iron Riboswitch. ACS Bio Med Chem Au
2022 c-AMP-GMP Tan, Z. et al.
 The Signaling Pathway That cGAMP Riboswitches Found: Analysis and Application of Riboswitches to Study cGAMP Signaling in Geobacter sulfurreducens. Int. J. Mol. Sci
2022 Adenine Dey, S. K. et al.
 Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag. Nat. Chem. Biol
2022 2'-dG Hamal, D. S., Panchapakesan, S. S. S., Slattery, P., Roth, A. & Breaker, R. R.
 Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2′-deoxyguanosine. Proc. Natl. Acad. Sci. U. S. A
2022 Guanine Hamal, D. S., Panchapakesan, S. S. S., Slattery, P., Roth, A. & Breaker, R. R.
 Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2′-deoxyguanosine. Proc. Natl. Acad. Sci. U. S. A
2022 Xanthine Hamal, D. S., Panchapakesan, S. S. S., Slattery, P., Roth, A. & Breaker, R. R.
 Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2′-deoxyguanosine. Proc. Natl. Acad. Sci. U. S. A
2022 Guanidine Fuks, C., Falkner, S., Schwierz, N. & Hengesbach, M.
 Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch. Front Mol Biosci
2022 Azaaromatic Trachman, R. J., 3rd, Passalacqua, L. F. M. & Ferré-D’Amaré, A. R.
 The bacterial yjdF riboswitch regulates translation through its tRNA-like fold. J. Biol. Chem
2022 TPP Zeller, M. J. et al.
 Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. ACS Chem. Biol
2022 TPP Zeller, M. J. et al.
 SHAPE-enabled fragment-based ligand discovery for RNA. Proc. Natl. Acad. Sci. U. S. A
2022 Glycine Hong, K.-Q., Zhang, J., Jin, B., Chen, T. & Wang, Z.-W.
 Development and characterization of a glycine biosensor system for fine-tuned metabolic regulation in Escherichia coli Microb. Cell Fact
2022 Li+ White, N., Sadeeshkumar, H., Sun, A., Sudarsan, N. & Breaker, R. R.
 Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes. Sci. Rep
2022 PreQ1 Schroeder, G. M. et al.
 A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nat. Commun
2022 Fluoride Yadav, R., Widom, J. R., Chauvier, A. & Walter, N. G.
 An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch. Nat. Commun
2022 SAM-III Chen, J., Zeng, Q., Wang, W., Sun, H., & Hu, G.
 Decoding the identification mechanism of an SAM-III riboswitch on ligands through multiple independent gaussian-accelerated molecular dynamics simulations. J. Chem. Inf. Model
2022 Na+ White, N., Sadeeshkumar, H., Sun, A., Sudarsan, N. & Breaker, R. R.
 Na riboswitches regulate genes for diverse physiological processes in bacteria. Nat. Chem. Biol
2022 MoCo Pavlova, N. & Penchovsky, R.
 Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics
2022 Wco Pavlova, N. & Penchovsky, R.
 Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics
2022 Magnesium Pavlova, N. & Penchovsky, R.
 Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics
2022 SAM-I_clan Traykovska, M., & Penchovsky, R.
 Targeting SAM-I riboswitch using antisense oligonucleotide technology for inhibiting the growth of staphylococcus aureus and listeria monocytogenes. Antibiotics
2023 SAM-I_clan Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A.
 Structure-based insights into recognition and regulation of SAM-sensing riboswitches. Sci China Life Sci
2023 SAM-II_clan Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A.
 Structure-based insights into recognition and regulation of SAM-sensing riboswitches. Sci China Life Sci
2023 SAM-III Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A.
 Structure-based insights into recognition and regulation of SAM-sensing riboswitches. Sci China Life Sci
2023 SAM-VI Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A.
 Structure-based insights into recognition and regulation of SAM-sensing riboswitches. Sci China Life Sci
2023 SAH Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A.
 Structure-based insights into recognition and regulation of SAM-sensing riboswitches. Sci China Life Sci
2023 SAM-SAH Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A.
 Structure-based insights into recognition and regulation of SAM-sensing riboswitches. Sci China Life Sci
2023 Lysine Marton Menendez, A. & Nesbitt, D. J.
 Ionic Cooperativity between Lysine and Potassium in the Lysine Riboswitch: Single-Molecule Kinetic and Thermodynamic Studies J. Phys. Chem
2023 SAM-SAH Hu, G., & Zhou, H. X.
 Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch. BioRxiv
2023 ZTP Bushhouse, D. Z. & Lucks, J. B.
 Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo Nucleic Acids Res
2023 SAM-VI Xue, Y., Li, J., Chen, D., Zhao, X., Hong, L., & Liu, Y.
 Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution. Nat. Commun
2023 MoCo Amadei, F., Reichenbach, M., Gallo, S. & Sigel, R. K. O.
 The structural features of the ligand-free moaA riboswitch and its ion-dependent folding. J. Inorg. Biochem
2023 Wco Amadei, F., Reichenbach, M., Gallo, S. & Sigel, R. K. O.
 The structural features of the ligand-free moaA riboswitch and its ion-dependent folding. J. Inorg. Biochem
2023 TPP Lee, H. K. et al.
 Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state. Structure
2023 THF Xu, L., Xiao, Y., Zhang, J. & Fang, X.
 Structural insights into translation regulation by the THF-II riboswitch. Nucleic Acids Res
2023 c-di-AMP Reich, S. J. et al.
 C-di-AMP Is a Second Messenger in Corynebacterium glutamicum That Regulates Expression of a Cell Wall-Related Peptidase via a Riboswitch. Microorganisms
2023 NAD+-II Xu, X. et al.
 Structure-based investigations of the NAD+-II riboswitch Nucleic Acids Res
2023 NAD+-II Peng, X., Liao, W., Lin, X., Lilley, D. M. J. & Huang, L.
 Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets Nucleic Acids Res
2023 Cobalamine Lennon, S. R. et al.
 Targeting Riboswitches with Beta-Axial-Substituted Cobalamins. ACS Chem. Biol