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Volumn 425, Issue 10, 2013, Pages 1596-1611

Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch

Author keywords

activity tuning; mutual information; riboswitch; RNA structure; transcriptional regulation

Indexed keywords

APTAMER; NUCLEOTIDE; PURINE;

EID: 84877582071     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.02.023     Document Type: Article
Times cited : (45)

References (72)
  • 1
    • 48249104039 scopus 로고    scopus 로고
    • Riboswitches: Emerging themes in RNA structure and function
    • R.K. Montange, and R.T. Batey Riboswitches: emerging themes in RNA structure and function Annu. Rev. Biophys. 37 2008 117 133
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 117-133
    • Montange, R.K.1    Batey, R.T.2
  • 2
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolite-binding riboswitches
    • A. Roth, and R.R. Breaker The structural and functional diversity of metabolite-binding riboswitches Annu. Rev. Biochem. 78 2009 305 334
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 305-334
    • Roth, A.1    Breaker, R.R.2
  • 3
    • 80052973462 scopus 로고    scopus 로고
    • Prospects for riboswitch discovery and analysis
    • R.R. Breaker Prospects for riboswitch discovery and analysis Mol. Cell 43 2011 867 879
    • (2011) Mol. Cell , vol.43 , pp. 867-879
    • Breaker, R.R.1
  • 4
    • 46349083026 scopus 로고    scopus 로고
    • The distributions, mechanisms, and structures of metabolite-binding riboswitches
    • J.E. Barrick, and R.R. Breaker The distributions, mechanisms, and structures of metabolite-binding riboswitches Genome Biol. 8 2007 R239
    • (2007) Genome Biol. , vol.8 , pp. 239
    • Barrick, J.E.1    Breaker, R.R.2
  • 5
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • M. Mandal, B. Boese, J.E. Barrick, W.C. Winkler, and R.R. Breaker Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria Cell 113 2003 577 586
    • (2003) Cell , vol.113 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 6
    • 34548726217 scopus 로고    scopus 로고
    • Ligand recognition determinants of guanine riboswitches
    • J. Mulhbacher, and D.A. Lafontaine Ligand recognition determinants of guanine riboswitches Nucleic Acids Res. 35 2007 5568 5580
    • (2007) Nucleic Acids Res. , vol.35 , pp. 5568-5580
    • Mulhbacher, J.1    Lafontaine, D.A.2
  • 7
    • 0031735563 scopus 로고    scopus 로고
    • The S box regulon: A new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria
    • F.J. Grundy, and T.M. Henkin The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria Mol. Microbiol. 30 1998 737 749
    • (1998) Mol. Microbiol. , vol.30 , pp. 737-749
    • Grundy, F.J.1    Henkin, T.M.2
  • 8
    • 0037453069 scopus 로고    scopus 로고
    • Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA
    • B.A. McDaniel, F.J. Grundy, I. Artsimovitch, and T.M. Henkin Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA Proc. Natl Acad. Sci. USA 100 2003 3083 3088
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 3083-3088
    • McDaniel, B.A.1    Grundy, F.J.2    Artsimovitch, I.3    Henkin, T.M.4
  • 9
    • 38649086717 scopus 로고    scopus 로고
    • Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in Bacillus subtilis exhibit differential sensitivity to SAM in vivo and in vitro
    • J. Tomsic, B.A. McDaniel, F.J. Grundy, and T.M. Henkin Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in Bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro J. Bacteriol. 190 2008 823 833
    • (2008) J. Bacteriol. , vol.190 , pp. 823-833
    • Tomsic, J.1    McDaniel, B.A.2    Grundy, F.J.3    Henkin, T.M.4
  • 11
    • 78649529299 scopus 로고    scopus 로고
    • SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch
    • C. Lu, F. Ding, A. Chowdhury, V. Pradhan, J. Tomsic, and W.M. Holmes SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch J. Mol. Biol. 404 2010 803 818
    • (2010) J. Mol. Biol. , vol.404 , pp. 803-818
    • Lu, C.1    Ding, F.2    Chowdhury, A.3    Pradhan, V.4    Tomsic, J.5    Holmes, W.M.6
  • 12
    • 33745628336 scopus 로고    scopus 로고
    • Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
    • R.K. Montange, and R.T. Batey Structure of the S-adenosylmethionine riboswitch regulatory mRNA element Nature 441 2006 1172 1175
    • (2006) Nature , vol.441 , pp. 1172-1175
    • Montange, R.K.1    Batey, R.T.2
  • 13
    • 38849103659 scopus 로고    scopus 로고
    • Purine sensing by riboswitches
    • J.N. Kim, and R.R. Breaker Purine sensing by riboswitches Biol. Cell 100 2008 1 11
    • (2008) Biol. Cell , vol.100 , pp. 1-11
    • Kim, J.N.1    Breaker, R.R.2
  • 14
    • 0842334528 scopus 로고    scopus 로고
    • Adenine riboswitches and gene activation by disruption of a transcription terminator
    • M. Mandal, and R.R. Breaker Adenine riboswitches and gene activation by disruption of a transcription terminator Nat. Struct. Mol. Biol. 11 2004 29 35
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 29-35
    • Mandal, M.1    Breaker, R.R.2
  • 15
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • R.T. Batey, S.D. Gilbert, and R.K. Montange Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine Nature 432 2004 411 415
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 16
    • 66349133602 scopus 로고    scopus 로고
    • Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs
    • S.D. Gilbert, F.E. Reyes, A.L. Edwards, and R.T. Batey Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs Structure 17 2009 857 868
    • (2009) Structure , vol.17 , pp. 857-868
    • Gilbert, S.D.1    Reyes, F.E.2    Edwards, A.L.3    Batey, R.T.4
  • 17
    • 33646768226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
    • S.D. Gilbert, C.D. Stoddard, S.J. Wise, and R.T. Batey Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain J. Mol. Biol. 359 2006 754 768
    • (2006) J. Mol. Biol. , vol.359 , pp. 754-768
    • Gilbert, S.D.1    Stoddard, C.D.2    Wise, S.J.3    Batey, R.T.4
  • 18
    • 13444271576 scopus 로고    scopus 로고
    • An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs
    • J. Noeske, C. Richter, M.A. Grundl, H.R. Nasiri, H. Schwalbe, and J. Wohnert An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs Proc. Natl Acad. Sci. USA 102 2005 1372 1377
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 1372-1377
    • Noeske, J.1    Richter, C.2    Grundl, M.A.3    Nasiri, H.R.4    Schwalbe, H.5    Wohnert, J.6
  • 19
    • 10644250950 scopus 로고    scopus 로고
    • Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs
    • A. Serganov, Y.R. Yuan, O. Pikovskaya, A. Polonskaia, L. Malinina, and A.T. Phan Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs Chem. Biol. 11 2004 1729 1741
    • (2004) Chem. Biol. , vol.11 , pp. 1729-1741
    • Serganov, A.1    Yuan, Y.R.2    Pikovskaya, O.3    Polonskaia, A.4    Malinina, L.5    Phan, A.T.6
  • 20
    • 36248982074 scopus 로고    scopus 로고
    • Mutational analysis of the purine riboswitch aptamer domain
    • S.D. Gilbert, C.E. Love, A.L. Edwards, and R.T. Batey Mutational analysis of the purine riboswitch aptamer domain Biochemistry 46 2007 13297 13309
    • (2007) Biochemistry , vol.46 , pp. 13297-13309
    • Gilbert, S.D.1    Love, C.E.2    Edwards, A.L.3    Batey, R.T.4
  • 22
    • 84865231710 scopus 로고    scopus 로고
    • Structure and mechanism of purine-binding riboswitches
    • R.T. Batey Structure and mechanism of purine-binding riboswitches Q. Rev. Biophys. 45 2012 345 381
    • (2012) Q. Rev. Biophys. , vol.45 , pp. 345-381
    • Batey, R.T.1
  • 23
    • 84862543748 scopus 로고    scopus 로고
    • RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs
    • J. Widmann, J. Stombaugh, D. McDonald, J. Chocholousova, P. Gardner, and M.K. Iyer RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs RNA 18 2012 1319 1327
    • (2012) RNA , vol.18 , pp. 1319-1327
    • Widmann, J.1    Stombaugh, J.2    McDonald, D.3    Chocholousova, J.4    Gardner, P.5    Iyer, M.K.6
  • 24
    • 58149138753 scopus 로고    scopus 로고
    • A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch
    • A.L. Edwards, and R.T. Batey A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch J. Mol. Biol. 385 2009 938 948
    • (2009) J. Mol. Biol. , vol.385 , pp. 938-948
    • Edwards, A.L.1    Batey, R.T.2
  • 25
    • 80052967464 scopus 로고    scopus 로고
    • Structural principles of nucleoside selectivity in a 2′- deoxyguanosine riboswitch
    • O. Pikovskaya, A. Polonskaia, D.J. Patel, and A. Serganov Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch Nat. Chem. Biol. 7 2011 748 755
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 748-755
    • Pikovskaya, O.1    Polonskaia, A.2    Patel, D.J.3    Serganov, A.4
  • 28
    • 79957851139 scopus 로고    scopus 로고
    • Sequence-based identification of 3D structural modules in RNA with RMDetect
    • J.A. Cruz, and E. Westhof Sequence-based identification of 3D structural modules in RNA with RMDetect Nat. Methods 8 2011 513 521
    • (2011) Nat. Methods , vol.8 , pp. 513-521
    • Cruz, J.A.1    Westhof, E.2
  • 29
    • 3042842115 scopus 로고    scopus 로고
    • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
    • A.A. Fodor, and R.W. Aldrich Influence of conservation on calculations of amino acid covariance in multiple sequence alignments Proteins 56 2004 211 221
    • (2004) Proteins , vol.56 , pp. 211-221
    • Fodor, A.A.1    Aldrich, R.W.2
  • 31
    • 33847308180 scopus 로고    scopus 로고
    • Core requirements of the adenine riboswitch aptamer for ligand binding
    • J.F. Lemay, and D.A. Lafontaine Core requirements of the adenine riboswitch aptamer for ligand binding RNA 13 2007 335 350
    • (2007) RNA , vol.13 , pp. 335-350
    • Lemay, J.F.1    Lafontaine, D.A.2
  • 33
    • 33845362968 scopus 로고    scopus 로고
    • Measuring covariation in RNA alignments: Physical realism improves information measures
    • S. Lindgreen, P.P. Gardner, and A. Krogh Measuring covariation in RNA alignments: physical realism improves information measures Bioinformatics 22 2006 2988 2995
    • (2006) Bioinformatics , vol.22 , pp. 2988-2995
    • Lindgreen, S.1    Gardner, P.P.2    Krogh, A.3
  • 34
    • 27944458910 scopus 로고    scopus 로고
    • Using information theory to search for co-evolving residues in proteins
    • L.C. Martin, G.B. Gloor, S.D. Dunn, and L.M. Wahl Using information theory to search for co-evolving residues in proteins Bioinformatics 21 2005 4116 4124
    • (2005) Bioinformatics , vol.21 , pp. 4116-4124
    • Martin, L.C.1    Gloor, G.B.2    Dunn, S.D.3    Wahl, L.M.4
  • 35
    • 60249099824 scopus 로고    scopus 로고
    • Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
    • J.G. Caporaso, S. Smit, B.C. Easton, L. Hunter, G.A. Huttley, and R. Knight Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics BMC Evol. Biol. 8 2008 327
    • (2008) BMC Evol. Biol. , vol.8 , pp. 327
    • Caporaso, J.G.1    Smit, S.2    Easton, B.C.3    Hunter, L.4    Huttley, G.A.5    Knight, R.6
  • 36
    • 41649108293 scopus 로고    scopus 로고
    • Ligand-dependent folding of the three-way junction in the purine riboswitch
    • C.D. Stoddard, S.D. Gilbert, and R.T. Batey Ligand-dependent folding of the three-way junction in the purine riboswitch RNA 14 2008 675 684
    • (2008) RNA , vol.14 , pp. 675-684
    • Stoddard, C.D.1    Gilbert, S.D.2    Batey, R.T.3
  • 38
    • 72149126118 scopus 로고    scopus 로고
    • A switch in time: Detailing the life of a riboswitch
    • A.D. Garst, and R.T. Batey A switch in time: detailing the life of a riboswitch Biochim. Biophys. Acta 1789 2009 584 591
    • (2009) Biochim. Biophys. Acta , vol.1789 , pp. 584-591
    • Garst, A.D.1    Batey, R.T.2
  • 39
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • J.K. Wickiser, M.T. Cheah, R.R. Breaker, and D.M. Crothers The kinetics of ligand binding by an adenine-sensing riboswitch Biochemistry 44 2005 13404 13414
    • (2005) Biochemistry , vol.44 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 40
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    • J.K. Wickiser, W.C. Winkler, R.R. Breaker, and D.M. Crothers The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch Mol. Cell 18 2005 49 60
    • (2005) Mol. Cell , vol.18 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 41
    • 79851499341 scopus 로고    scopus 로고
    • Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms
    • J.F. Lemay, G. Desnoyers, S. Blouin, B. Heppell, L. Bastet, and P. St-Pierre Comparative study between transcriptionally- and translationally- acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms PLoS Genet. 7 2011 e1001278
    • (2011) PLoS Genet. , vol.7 , pp. 1001278
    • Lemay, J.F.1    Desnoyers, G.2    Blouin, S.3    Heppell, B.4    Bastet, L.5    St-Pierre, P.6
  • 42
    • 0028227702 scopus 로고
    • The RNA chain elongation rate in Escherichia coli depends on the growth rate
    • U. Vogel, and K.F. Jensen The RNA chain elongation rate in Escherichia coli depends on the growth rate J. Bacteriol. 176 1994 2807 2813
    • (1994) J. Bacteriol. , vol.176 , pp. 2807-2813
    • Vogel, U.1    Jensen, K.F.2
  • 43
    • 77951589688 scopus 로고    scopus 로고
    • Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    • S. Proshkin, A.R. Rahmouni, A. Mironov, and E. Nudler Cooperation between translating ribosomes and RNA polymerase in transcription elongation Science 328 2010 504 508
    • (2010) Science , vol.328 , pp. 504-508
    • Proshkin, S.1    Rahmouni, A.R.2    Mironov, A.3    Nudler, E.4
  • 44
    • 84866340759 scopus 로고    scopus 로고
    • Insights into the regulatory landscape of the lysine riboswitch
    • A.D. Garst, E.B. Porter, and R.T. Batey Insights into the regulatory landscape of the lysine riboswitch J. Mol. Biol 423 2012 17 33
    • (2012) J. Mol. Biol , vol.423 , pp. 17-33
    • Garst, A.D.1    Porter, E.B.2    Batey, R.T.3
  • 45
    • 84857771826 scopus 로고    scopus 로고
    • Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch
    • G.A. Perdrizet 2nd, I. Artsimovitch, R. Furman, T.R. Sosnick, and T. Pan Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch Proc. Natl Acad. Sci. USA 109 2012 3323 3328
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 3323-3328
    • Perdrizet II, G.A.1    Artsimovitch, I.2    Furman, R.3    Sosnick, T.R.4    Pan, T.5
  • 46
    • 80054074740 scopus 로고    scopus 로고
    • The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer
    • J.J. Trausch, P. Ceres, F.E. Reyes, and R.T. Batey The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer Structure 19 2011 1413 1423
    • (2011) Structure , vol.19 , pp. 1413-1423
    • Trausch, J.J.1    Ceres, P.2    Reyes, F.E.3    Batey, R.T.4
  • 47
    • 33750712046 scopus 로고    scopus 로고
    • Modified pyrimidines specifically bind the purine riboswitch
    • S.D. Gilbert, S.J. Mediatore, and R.T. Batey Modified pyrimidines specifically bind the purine riboswitch J. Am. Chem. Soc. 128 2006 14214 14215
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 14214-14215
    • Gilbert, S.D.1    Mediatore, S.J.2    Batey, R.T.3
  • 48
    • 0032300804 scopus 로고    scopus 로고
    • Conserved geometrical base-pairing patterns in RNA
    • N.B. Leontis, and E. Westhof Conserved geometrical base-pairing patterns in RNA Q. Rev. Biophys. 31 1998 399 455
    • (1998) Q. Rev. Biophys. , vol.31 , pp. 399-455
    • Leontis, N.B.1    Westhof, E.2
  • 49
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)
    • E.J. Merino, K.A. Wilkinson, J.L. Coughlan, and K.M. Weeks RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE) J. Am. Chem. Soc. 127 2005 4223 4231
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 50
    • 33947720028 scopus 로고    scopus 로고
    • Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution
    • K.A. Wilkinson, E.J. Merino, and K.M. Weeks Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution Nat. Protoc. 1 2006 1610 1616
    • (2006) Nat. Protoc. , vol.1 , pp. 1610-1616
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 52
    • 51949099863 scopus 로고    scopus 로고
    • Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA
    • C.M. Gherghe, Z. Shajani, K.A. Wilkinson, G. Varani, and K.M. Weeks Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA J. Am. Chem. Soc. 130 2008 12244 12245
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 12244-12245
    • Gherghe, C.M.1    Shajani, Z.2    Wilkinson, K.A.3    Varani, G.4    Weeks, K.M.5
  • 53
    • 80053542128 scopus 로고    scopus 로고
    • A powerful approach for the selection of 2-aminopurine substitution sites to investigate RNA folding
    • M.F. Souliere, A. Haller, R. Rieder, and R. Micura A powerful approach for the selection of 2-aminopurine substitution sites to investigate RNA folding J. Am. Chem. Soc. 133 2011 16161 16167
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 16161-16167
    • Souliere, M.F.1    Haller, A.2    Rieder, R.3    Micura, R.4
  • 55
    • 80455178803 scopus 로고    scopus 로고
    • Molecular sensing by the aptamer domain of the FMN riboswitch: A general model for ligand binding by conformational selection
    • Q. Vicens, E. Mondragon, and R.T. Batey Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection Nucleic Acids Res. 39 2011 8586 8598
    • (2011) Nucleic Acids Res. , vol.39 , pp. 8586-8598
    • Vicens, Q.1    Mondragon, E.2    Batey, R.T.3
  • 56
    • 0042890402 scopus 로고    scopus 로고
    • Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL)
    • L.E. Johansen, P. Nygaard, C. Lassen, Y. Agerso, and H.H. Saxild Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL) J. Bacteriol. 185 2003 5200 5209
    • (2003) J. Bacteriol. , vol.185 , pp. 5200-5209
    • Johansen, L.E.1    Nygaard, P.2    Lassen, C.3    Agerso, Y.4    Saxild, H.H.5
  • 57
    • 36048942754 scopus 로고    scopus 로고
    • Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine
    • J.N. Kim, A. Roth, and R.R. Breaker Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine Proc. Natl Acad. Sci. USA 104 2007 16092 16097
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 16092-16097
    • Kim, J.N.1    Roth, A.2    Breaker, R.R.3
  • 58
    • 84857080591 scopus 로고    scopus 로고
    • Functional complexity and regulation through RNA dynamics
    • E.A. Dethoff, J. Chugh, A.M. Mustoe, and H.M. Al-Hashimi Functional complexity and regulation through RNA dynamics Nature 482 2012 322 330
    • (2012) Nature , vol.482 , pp. 322-330
    • Dethoff, E.A.1    Chugh, J.2    Mustoe, A.M.3    Al-Hashimi, H.M.4
  • 61
    • 84860160810 scopus 로고    scopus 로고
    • Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy
    • B. Chen, X. Zuo, Y.X. Wang, and T.K. Dayie Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy Nucleic Acids Res. 40 2012 3117 3130
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3117-3130
    • Chen, B.1    Zuo, X.2    Wang, Y.X.3    Dayie, T.K.4
  • 62
    • 79953060592 scopus 로고    scopus 로고
    • Cooperative and directional folding of the preQ1 riboswitch aptamer domain
    • J. Feng, N.G. Walter, and C.L. Brooks 3rd. Cooperative and directional folding of the preQ1 riboswitch aptamer domain J. Am. Chem. Soc. 133 2011 4196 4199
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 4196-4199
    • Feng, J.1    Walter, N.G.2    Brooks III, C.L.3
  • 63
    • 77955315020 scopus 로고    scopus 로고
    • RNA dynamics by design: Biasing ensembles towards the ligand-bound state
    • A.C. Stelzer, J.D. Kratz, Q. Zhang, and H.M. Al-Hashimi RNA dynamics by design: biasing ensembles towards the ligand-bound state Angew. Chem. 49 2010 5731 5733
    • (2010) Angew. Chem. , vol.49 , pp. 5731-5733
    • Stelzer, A.C.1    Kratz, J.D.2    Zhang, Q.3    Al-Hashimi, H.M.4
  • 65
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • T.D. Schneider, and R.M. Stephens Sequence logos: a new way to display consensus sequences Nucleic Acids Res. 18 1990 6097 6100
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 66
    • 77955465509 scopus 로고    scopus 로고
    • Using a riboswitch sensor to examine coenzyme B(12) metabolism and transport in E. coli
    • C.C. Fowler, E.D. Brown, and Y. Li Using a riboswitch sensor to examine coenzyme B(12) metabolism and transport in E. coli Chem. Biol. 17 2010 756 765
    • (2010) Chem. Biol. , vol.17 , pp. 756-765
    • Fowler, C.C.1    Brown, E.D.2    Li, Y.3
  • 67
    • 31544450286 scopus 로고    scopus 로고
    • Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
    • T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, and M. Baba Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 2 2006 0008
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 0008
    • Baba, T.1    Ara, T.2    Hasegawa, M.3    Takai, Y.4    Okumura, Y.5    Baba, M.6
  • 68
    • 11844290117 scopus 로고    scopus 로고
    • The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-box (XptR) regulons by adjusting the purine base pool size
    • P. Nygaard, and H.H. Saxild The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-box (XptR) regulons by adjusting the purine base pool size J. Bacteriol. 187 2005 791 794
    • (2005) J. Bacteriol. , vol.187 , pp. 791-794
    • Nygaard, P.1    Saxild, H.H.2
  • 72
    • 13944278373 scopus 로고    scopus 로고
    • SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • R. Das, A. Laederach, S.M. Pearlman, D. Herschlag, and R.B. Altman SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments RNA 11 2005 344 354
    • (2005) RNA , vol.11 , pp. 344-354
    • Das, R.1    Laederach, A.2    Pearlman, S.M.3    Herschlag, D.4    Altman, R.B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.