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Regulation of bacterial gene expression by riboswitches
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Winkler W.C., and Breaker R.R. Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 59 (2005) 487-517
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Riboswitches as versatile gene control elements
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Tucker B.J., and Breaker R.R. Riboswitches as versatile gene control elements. Curr Opin Struct Biol 15 (2005) 342-348
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Curr Opin Struct Biol
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Tucker, B.J.1
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33744469562
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Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
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The recently published TPP riboswitch crystal structure, which provides mechanistic information on riboswitch folding and antibiotic resistance.
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Thore S., Leibundgut M., and Ban N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312 (2006) 1208-1211. The recently published TPP riboswitch crystal structure, which provides mechanistic information on riboswitch folding and antibiotic resistance.
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Thore, S.1
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Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs
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Serganov A., Yuan Y.R., Pikovskaya O., Polonskaia A., Malinina L., Phan A.T., Hobartner C., Micura R., Breaker R.R., and Patel D.J. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol 11 (2004) 1729-1741
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Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
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The recently published TPP riboswitch crystal structure is complemented by enzymatic probing data.
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Serganov A., Polonskaia A., Phan A.T., Breaker R.R., and Patel D.J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441 (2006) 1167-1171. The recently published TPP riboswitch crystal structure is complemented by enzymatic probing data.
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Serganov, A.1
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Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
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Batey R.T., Gilbert S.D., and Montange R.K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432 (2004) 411-415
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Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
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Crystal structures of both pre-cleavage and post-cleavage of the glmS riboswitch. Structural alignment of the ligand suggests general acid-base catalysis for the cleavage mechanism.
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Klein D.J., and Ferre-D'Amare A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313 (2006) 1752-1756. Crystal structures of both pre-cleavage and post-cleavage of the glmS riboswitch. Structural alignment of the ligand suggests general acid-base catalysis for the cleavage mechanism.
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Science
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Klein, D.J.1
Ferre-D'Amare, A.R.2
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Crystal structures of the Thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition
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Edwards T.E., and Ferre-D'Amdre A.R. Crystal structures of the Thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14 (2006) 1459-1468
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Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
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Montage R.K., and Batey R.T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441 (2006) 1172-1175
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An artificial riboswitch for controlling pre-mRNA splicing
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Kim D.S., Gusti V., Pillai S.G., and Gaur R.K. An artificial riboswitch for controlling pre-mRNA splicing. RNA 11 (2005) 1667-1677
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Kim, D.S.1
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33644792751
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The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase
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A new SAM-binding riboswitch that controls expression through translation repression. Mutational data suggest indistinct aptamer and expression platform regions.
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Fuchs R.T., Grundy F.J., and Henkin T.M. The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat Struct Mol Biol 13 (2006) 226-233. A new SAM-binding riboswitch that controls expression through translation repression. Mutational data suggest indistinct aptamer and expression platform regions.
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Nat Struct Mol Biol
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Fuchs, R.T.1
Grundy, F.J.2
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Riboswitches and the role of noncoding RNAs in bacterial metabolic control
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Winkler W.C. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol 9 (2005) 594-602
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Curr Opin Chem Biol
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Flipping riboswitches
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Nudler E. Flipping riboswitches. Cell 126 (2006) 19-22
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Structures of regulatory elements in mRNAs
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Batey R.T. Structures of regulatory elements in mRNAs. Curr Opin Struct Biol 16 (2006) 299-306
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Tandem riboswitch architectures exhibit complex gene control functions
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Tandem riboswitches within one 5′-UTR respond to different metabolites, exerting a higher level of genetic control.
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Sudarsan N., Hammond M.C., Block K.F., Welz R., Barrick J.E., Roth A., and Breaker R.R. Tandem riboswitch architectures exhibit complex gene control functions. Science 314 (2006) 300-304. Tandem riboswitches within one 5′-UTR respond to different metabolites, exerting a higher level of genetic control.
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Science
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Sudarsan, N.1
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Metal ions and RNA folding: a highly charged topic with a dynamic future
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Woodson S.A. Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr Opin Chem Biol 9 (2005) 104-109
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A guide to ions and RNA structure
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Draper D.E. A guide to ions and RNA structure. RNA 10 (2004) 335-343
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2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures
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2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc Natl Acad Sci USA 103 (2006) 14003-14008
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Proc Natl Acad Sci USA
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Grilley, D.1
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Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
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The aptamer domain pre-folds before ligand binding, and its structure reorganizes after ligand binding, suggesting a two-step model for riboswitch binding.
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Gilbert S.D., Stoddard C.D., Wise S.J., and Batey R.T. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol 359 (2006) 754-768. The aptamer domain pre-folds before ligand binding, and its structure reorganizes after ligand binding, suggesting a two-step model for riboswitch binding.
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Gilbert, S.D.1
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Folding of the adenine riboswitch
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Lemay J.F., Penedo J.C., Tremblay R., Lilley D.M., and Lafontaine D.A. Folding of the adenine riboswitch. Chem Biol 13 (2006) 857-868
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Control of gene expression by a natural metabolite-responsive ribozyme
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Winkler W.C., Nahvi A., Roth A., Collins J.A., and Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 (2004) 281-286
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Nature
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Winkler, W.C.1
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Evidence for preorganization of the glmS ribozyme ligand binding pocket
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Hampel K.J., and Tinsley M.M. Evidence for preorganization of the glmS ribozyme ligand binding pocket. Biochemistry 45 (2006) 7861-7871
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Biochemistry
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Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions
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Roth A., Nahvi A., Lee M., Jona I., and Breaker R.R. Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA 12 (2006) 607-619
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The pleiotropic two-component regulatory system PhoP-PhoQ
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The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
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The first experimental evidence showing a connection between the kinetics of ligand binding and transcription. The effects of the NusA protein highlight the importance of pause sites.
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Wickiser J.K., Winkler W.C., Breaker R.R., and Crothers D.M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 18 (2005) 49-60. The first experimental evidence showing a connection between the kinetics of ligand binding and transcription. The effects of the NusA protein highlight the importance of pause sites.
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The kinetics of ligand binding by an adenine-sensing riboswitch
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The association and dissociation rates of adenine, 2-aminopurine, and 2,6-diaminopurine binding to the adenine riboswitch are compared. The data are interpreted in terms of kinetic or thermodynamic control mechanisms.
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Wickiser J.K., Cheah M.T., Breaker R.R., and Crothers D.M. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44 (2005) 13404-13414. The association and dissociation rates of adenine, 2-aminopurine, and 2,6-diaminopurine binding to the adenine riboswitch are compared. The data are interpreted in terms of kinetic or thermodynamic control mechanisms.
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Biochemistry
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Wickiser, J.K.1
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33845971464
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Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae
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2+- and glycine-dependent folding transitions and draw conclusions on how the two events energetically contribute to the riboswitch structure.
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2+- and glycine-dependent folding transitions and draw conclusions on how the two events energetically contribute to the riboswitch structure.
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Lipfert, J.1
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Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
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2+ ions do not contribute to structural changes upon addition and are not essential for ligand binding.
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2+ ions do not contribute to structural changes upon addition and are not essential for ligand binding.
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Noeske, J.1
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