메뉴 건너뛰기




Volumn 1839, Issue 10, 2014, Pages 919-930

The purine riboswitch as a model system for exploring RNA biology and chemistry

Author keywords

Co transcriptional folding; Gene expression; Purine; Riboswitch; RNA structure

Indexed keywords

ADENINE; APTAMER; DEOXYGUANOSINE; FLAVINE MONONUCLEOTIDE; GUANINE; PURINE;

EID: 84908067664     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2014.02.014     Document Type: Review
Times cited : (29)

References (130)
  • 2
    • 53549089576 scopus 로고    scopus 로고
    • Crystal structure of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism
    • Lu C., Smith A.M., Fuch R.T., Ding F., Rajashankar K., Henkin T.M., Ke A. Crystal structure of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat. Struct. Mol. Biol. 2008, 15:1076-1083.
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 1076-1083
    • Lu, C.1    Smith, A.M.2    Fuch, R.T.3    Ding, F.4    Rajashankar, K.5    Henkin, T.M.6    Ke, A.7
  • 3
    • 84870539710 scopus 로고    scopus 로고
    • B12 cofactors directly stabilize an mRNA regulatory switch
    • Johnson J.E., Reyes F.E., Polaski J.T., Batey R.T. B12 cofactors directly stabilize an mRNA regulatory switch. Nature 2012, 492:133-137.
    • (2012) Nature , vol.492 , pp. 133-137
    • Johnson, J.E.1    Reyes, F.E.2    Polaski, J.T.3    Batey, R.T.4
  • 4
    • 33745628336 scopus 로고    scopus 로고
    • Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
    • Montange R.K., Batey R.T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 2006, 441:1172-1175.
    • (2006) Nature , vol.441 , pp. 1172-1175
    • Montange, R.K.1    Batey, R.T.2
  • 5
    • 33744469562 scopus 로고    scopus 로고
    • Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
    • Thore S., Leibundgut M., Ban N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 2006, 312:1208-1211.
    • (2006) Science , vol.312 , pp. 1208-1211
    • Thore, S.1    Leibundgut, M.2    Ban, N.3
  • 6
    • 33745635350 scopus 로고    scopus 로고
    • Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
    • 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, 441:1167-1171.
    • (2006) Nature , vol.441 , pp. 1167-1171
    • Serganov, A.1    Polonskaia, A.2    Phan, A.T.3    Breaker, R.R.4    Patel, D.J.5
  • 7
    • 62049086072 scopus 로고    scopus 로고
    • Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase
    • Klein D.J., Edwards T.E., Ferre-D'Amare A.R. Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat. Struct. Mol. Biol. 2009, 16:343-344.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 343-344
    • Klein, D.J.1    Edwards, T.E.2    Ferre-D'Amare, A.R.3
  • 8
    • 62549154008 scopus 로고    scopus 로고
    • Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA
    • 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, 33:784-790.
    • (2009) Mol. Cell , vol.33 , pp. 784-790
    • Kang, M.1    Peterson, R.2    Feigon, J.3
  • 9
    • 66449089224 scopus 로고    scopus 로고
    • The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain
    • Spitale R.C., Torelli A.T., Krucinska J., Bandarian V., Wedekind J.E. The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J. Biol. Chem. 2009, 284:11012-11016.
    • (2009) J. Biol. Chem. , vol.284 , pp. 11012-11016
    • Spitale, R.C.1    Torelli, A.T.2    Krucinska, J.3    Bandarian, V.4    Wedekind, J.E.5
  • 10
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • Batey R.T., Gilbert S.D., Montange R.K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 2004, 432:411-415.
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 12
    • 0030894628 scopus 로고    scopus 로고
    • 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
    • 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, 179:2540-2550.
    • (1997) J. Bacteriol. , vol.179 , pp. 2540-2550
    • Christiansen, L.C.1    Schou, S.2    Nygaard, P.3    Saxild, H.H.4
  • 13
    • 0021217722 scopus 로고
    • Stability of an RNA secondary structure affects in vitro transcription pausing in the trp operon leader region
    • Landick R., Yanofsky C. Stability of an RNA secondary structure affects in vitro transcription pausing in the trp operon leader region. J. Biol. Chem. 1984, 259:1550-1555.
    • (1984) J. Biol. Chem. , vol.259 , pp. 1550-1555
    • Landick, R.1    Yanofsky, C.2
  • 14
    • 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
    • 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. 1998, 30:737-749.
    • (1998) Mol. Microbiol. , vol.30 , pp. 737-749
    • Grundy, F.J.1    Henkin, T.M.2
  • 15
    • 0035859828 scopus 로고    scopus 로고
    • A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria
    • Miranda-Rios J., Navarro M., Soberon 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. 2001, 98:9736-9741.
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 9736-9741
    • Miranda-Rios, J.1    Navarro, M.2    Soberon, M.3
  • 16
    • 0033230755 scopus 로고    scopus 로고
    • A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes
    • 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, 15:439-442.
    • (1999) Trends Genet. , vol.15 , pp. 439-442
    • Gelfand, M.S.1    Mironov, A.A.2    Jomantas, J.3    Kozlov, Y.I.4    Perumov, D.A.5
  • 17
    • 0034691163 scopus 로고    scopus 로고
    • Adenosylcobalamin inhibits ribosome binding to btuB RNA
    • Nou X., Kadner R.J. Adenosylcobalamin inhibits ribosome binding to btuB RNA. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:7190-7195.
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 7190-7195
    • Nou, X.1    Kadner, R.J.2
  • 18
    • 0035859803 scopus 로고    scopus 로고
    • Do mRNAs act as direct sensors of small molecules to control their expression?
    • Stormo G.D., Ji Y. Do mRNAs act as direct sensors of small molecules to control their expression?. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:9465-9467.
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 9465-9467
    • Stormo, G.D.1    Ji, Y.2
  • 19
    • 0038476616 scopus 로고    scopus 로고
    • The riboswitch-mediated control of sulfur metabolism in bacteria
    • Epshtein V., Mironov A.S., Nudler E. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:5052-5056.
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 5052-5056
    • Epshtein, V.1    Mironov, A.S.2    Nudler, E.3
  • 20
    • 0037453069 scopus 로고    scopus 로고
    • Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA
    • McDaniel B.A., Grundy F.J., Artsimovitch I., Henkin T.M. 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, 100:3083-3088.
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 3083-3088
    • McDaniel, B.A.1    Grundy, F.J.2    Artsimovitch, I.3    Henkin, T.M.4
  • 24
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • 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, 113:577-586.
    • (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
  • 26
    • 36048942754 scopus 로고    scopus 로고
    • Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine
    • 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, 104:16092-16097.
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 16092-16097
    • Kim, J.N.1    Roth, A.2    Breaker, R.R.3
  • 27
    • 70350107533 scopus 로고    scopus 로고
    • Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold
    • de la Pena M., Dufour D., Gallego J. Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold. RNA 2009, 15:1949-1964.
    • (2009) RNA , vol.15 , pp. 1949-1964
    • de la Pena, M.1    Dufour, D.2    Gallego, J.3
  • 28
    • 29844453234 scopus 로고    scopus 로고
    • Topology of three-way junctions in folded RNAs
    • Lescoute A., Westhof E. Topology of three-way junctions in folded RNAs. RNA 2006, 12:83-93.
    • (2006) RNA , vol.12 , pp. 83-93
    • Lescoute, A.1    Westhof, E.2
  • 30
    • 80052967464 scopus 로고    scopus 로고
    • Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch
    • Pikovskaya O., Polonskaia A., Patel D.J., Serganov A. Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch. Nat. Chem. Biol. 2011, 7:748-755.
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 748-755
    • Pikovskaya, O.1    Polonskaia, A.2    Patel, D.J.3    Serganov, A.4
  • 31
    • 0842334528 scopus 로고    scopus 로고
    • Adenine riboswitches and gene activation by disruption of a transcription terminator
    • Mandal M., Breaker R.R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol. 2004, 11:29-35.
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 29-35
    • Mandal, M.1    Breaker, R.R.2
  • 34
    • 66349133602 scopus 로고    scopus 로고
    • Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs
    • 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, 17:857-868.
    • (2009) Structure , vol.17 , pp. 857-868
    • Gilbert, S.D.1    Reyes, F.E.2    Edwards, A.L.3    Batey, R.T.4
  • 35
    • 58149138753 scopus 로고    scopus 로고
    • A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch
    • Edwards A.L., Batey R.T. A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J. Mol. Biol. 2009, 385:938-948.
    • (2009) J. Mol. Biol. , vol.385 , pp. 938-948
    • Edwards, A.L.1    Batey, R.T.2
  • 37
    • 84879103214 scopus 로고    scopus 로고
    • Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold
    • 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, 9:353-355.
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 353-355
    • Liberman, J.A.1    Salim, M.2    Krucinska, J.3    Wedekind, J.E.4
  • 38
    • 0030752211 scopus 로고    scopus 로고
    • Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
    • Zimmermann G.R., Jenison R.D., Wick C.L., Simorre J.P., Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat. Struct. Biol. 1997, 4:644-649.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 644-649
    • Zimmermann, G.R.1    Jenison, R.D.2    Wick, C.L.3    Simorre, J.P.4    Pardi, A.5
  • 39
    • 84855724406 scopus 로고    scopus 로고
    • Recognition of S-adenosylmethionine by riboswitches
    • Batey R.T. Recognition of S-adenosylmethionine by riboswitches. Wiley Interdiscip. Rev. RNA 2011, 2:299-311.
    • (2011) Wiley Interdiscip. Rev. RNA , vol.2 , pp. 299-311
    • Batey, R.T.1
  • 40
    • 84865231710 scopus 로고    scopus 로고
    • Structure and mechanism of purine-binding riboswitches
    • Batey R.T. Structure and mechanism of purine-binding riboswitches. Q. Rev. Biophys. 2012, 45:345-381.
    • (2012) Q. Rev. Biophys. , vol.45 , pp. 345-381
    • Batey, R.T.1
  • 41
    • 30944458838 scopus 로고    scopus 로고
    • Atomic level architecture of group I introns revealed
    • Vicens Q., Cech T.R. Atomic level architecture of group I introns revealed. Trends Biochem. Sci. 2006, 31:41-51.
    • (2006) Trends Biochem. Sci. , vol.31 , pp. 41-51
    • Vicens, Q.1    Cech, T.R.2
  • 43
    • 33646768226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
    • 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, 359:754-768.
    • (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
  • 44
    • 73449116019 scopus 로고    scopus 로고
    • Design and antimicrobial action of purine analogues that bind guanine riboswitches
    • Kim J.N., Blount K.F., Puskarz I., Lim J., Link K.H., Breaker R.R. Design and antimicrobial action of purine analogues that bind guanine riboswitches. ACS Chem. Biol. 2009, 4:915-927.
    • (2009) ACS Chem. Biol. , vol.4 , pp. 915-927
    • Kim, J.N.1    Blount, K.F.2    Puskarz, I.3    Lim, J.4    Link, K.H.5    Breaker, R.R.6
  • 45
    • 33750712046 scopus 로고    scopus 로고
    • Modified pyrimidines specifically bind the purine riboswitch
    • Gilbert S.D., Mediatore S.J., Batey R.T. Modified pyrimidines specifically bind the purine riboswitch. J. Am. Chem. Soc. 2006, 128:14214-14215.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 14214-14215
    • Gilbert, S.D.1    Mediatore, S.J.2    Batey, R.T.3
  • 47
    • 33847308180 scopus 로고    scopus 로고
    • Core requirements of the adenine riboswitch aptamer for ligand binding
    • Lemay J.F., Lafontaine D.A. Core requirements of the adenine riboswitch aptamer for ligand binding. RNA 2007, 13:339-350.
    • (2007) RNA , vol.13 , pp. 339-350
    • Lemay, J.F.1    Lafontaine, D.A.2
  • 48
    • 84877582071 scopus 로고    scopus 로고
    • Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch
    • Stoddard C.D., Widmann J., Trausch J.J., Marcano-Velazquez J.G., Knight R., Batey R.T. Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch. J. Mol. Biol. 2013, 425:1596-1611.
    • (2013) J. Mol. Biol. , vol.425 , pp. 1596-1611
    • Stoddard, C.D.1    Widmann, J.2    Trausch, J.J.3    Marcano-Velazquez, J.G.4    Knight, R.5    Batey, R.T.6
  • 49
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • Wickiser J.K., Cheah M.T., Breaker R.R., Crothers D.M. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 2005, 44:13404-13414.
    • (2005) Biochemistry , vol.44 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 50
    • 33845700514 scopus 로고    scopus 로고
    • Riboswitches as antibacterial drug targets
    • Blount K.F., Breaker R.R. Riboswitches as antibacterial drug targets. Nat. Biotechnol. 2006, 24:1558-1564.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1558-1564
    • Blount, K.F.1    Breaker, R.R.2
  • 51
    • 41649108293 scopus 로고    scopus 로고
    • Ligand-dependent folding of the three-way junction in the purine riboswitch
    • Stoddard C.D., Gilbert S.D., Batey R.T. Ligand-dependent folding of the three-way junction in the purine riboswitch. RNA 2008, 14:675-684.
    • (2008) RNA , vol.14 , pp. 675-684
    • Stoddard, C.D.1    Gilbert, S.D.2    Batey, R.T.3
  • 53
    • 36248982074 scopus 로고    scopus 로고
    • Mutational analysis of the purine riboswitch aptamer domain
    • Gilbert S.D., Love C.E., Edwards A.L., Batey R.T. Mutational analysis of the purine riboswitch aptamer domain. Biochemistry 2007, 46:13297-13309.
    • (2007) Biochemistry , vol.46 , pp. 13297-13309
    • Gilbert, S.D.1    Love, C.E.2    Edwards, A.L.3    Batey, R.T.4
  • 56
    • 77749304812 scopus 로고    scopus 로고
    • Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine
    • Brenner M.D., Scanlan M.S., Nahas M.K., Ha T., Silverman S.K. Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. Biochemistry 2010, 49:1596-1605.
    • (2010) Biochemistry , vol.49 , pp. 1596-1605
    • Brenner, M.D.1    Scanlan, M.S.2    Nahas, M.K.3    Ha, T.4    Silverman, S.K.5
  • 57
    • 33846898497 scopus 로고    scopus 로고
    • Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
    • Noeske J., Buck J., Furtig B., Nasiri H.R., Schwalbe H., Wohnert J. Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res. 2007, 35:572-583.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 572-583
    • Noeske, J.1    Buck, J.2    Furtig, B.3    Nasiri, H.R.4    Schwalbe, H.5    Wohnert, J.6
  • 58
    • 33747367748 scopus 로고    scopus 로고
    • Riboswitches: fold and function
    • Gilbert S.D., Batey R.T. Riboswitches: fold and function. Chem. Biol. 2006, 13:805-807.
    • (2006) Chem. Biol. , vol.13 , pp. 805-807
    • Gilbert, S.D.1    Batey, R.T.2
  • 59
    • 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
    • Noeske J., Richter C., Grundl M.A., Nasiri H.R., Schwalbe H., Wohnert J. An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:1372-1377.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , 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
  • 60
    • 34548587016 scopus 로고    scopus 로고
    • Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain
    • Noeske J., Schwalbe H., Wohnert J. Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain. Nucleic Acids Res. 2007, 35:5262-5273.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 5262-5273
    • Noeske, J.1    Schwalbe, H.2    Wohnert, J.3
  • 61
    • 33845942987 scopus 로고    scopus 로고
    • The adenine riboswitch: a new gene regulation mechanism
    • Lemay J.F., Lafontaine D.A. The adenine riboswitch: a new gene regulation mechanism. Med. Sci. (Paris) 2006, 22:1053-1059.
    • (2006) Med. Sci. (Paris) , vol.22 , pp. 1053-1059
    • Lemay, J.F.1    Lafontaine, D.A.2
  • 63
    • 1242274330 scopus 로고    scopus 로고
    • A guide to ions and RNA structure
    • Draper D.E. A guide to ions and RNA structure. RNA 2004, 10:335-343.
    • (2004) RNA , vol.10 , pp. 335-343
    • Draper, D.E.1
  • 64
    • 33748300801 scopus 로고    scopus 로고
    • Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition
    • Edwards T.E., Ferre-D'Amare A.R. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 2006, 14:1459-1468.
    • (2006) Structure , vol.14 , pp. 1459-1468
    • Edwards, T.E.1    Ferre-D'Amare, A.R.2
  • 65
    • 62249156218 scopus 로고    scopus 로고
    • Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch
    • Serganov A., Huang L., Patel D.J. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature 2009, 458:233-237.
    • (2009) Nature , vol.458 , pp. 233-237
    • Serganov, A.1    Huang, L.2    Patel, D.J.3
  • 66
    • 80455178803 scopus 로고    scopus 로고
    • Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection
    • Vicens Q., Mondragon 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, 39:8586-8598.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 8586-8598
    • Vicens, Q.1    Mondragon, E.2    Batey, R.T.3
  • 67
  • 68
    • 79953052076 scopus 로고    scopus 로고
    • Structural basis of cooperative ligand binding by the glycine riboswitch
    • Butler E.B., Xiong Y., Wang J., Strobel S.A. Structural basis of cooperative ligand binding by the glycine riboswitch. Chem. Biol. 2011, 18:293-298.
    • (2011) Chem. Biol. , vol.18 , pp. 293-298
    • Butler, E.B.1    Xiong, Y.2    Wang, J.3    Strobel, S.A.4
  • 70
    • 78649970557 scopus 로고    scopus 로고
    • Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch
    • Huang L., Serganov A., Patel D.J. Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol. Cell 2010, 40:774-786.
    • (2010) Mol. Cell , vol.40 , pp. 774-786
    • Huang, L.1    Serganov, A.2    Patel, D.J.3
  • 71
    • 0036786231 scopus 로고    scopus 로고
    • Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly
    • Batey R.T., Doudna J.A. Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly. Biochemistry 2002, 41:11703-11710.
    • (2002) Biochemistry , vol.41 , pp. 11703-11710
    • Batey, R.T.1    Doudna, J.A.2
  • 72
    • 77955081034 scopus 로고    scopus 로고
    • 2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain
    • 2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res. 2010, 38:4143-4153.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4143-4153
    • Buck, J.1    Noeske, J.2    Wohnert, J.3    Schwalbe, H.4
  • 73
    • 79953682254 scopus 로고    scopus 로고
    • 2+ on the free energy landscape for folding a purine riboswitch RNA
    • 2+ on the free energy landscape for folding a purine riboswitch RNA. Biochemistry 2011, 50:2790-2799.
    • (2011) Biochemistry , vol.50 , pp. 2790-2799
    • Leipply, D.1    Draper, D.E.2
  • 74
    • 67649359324 scopus 로고    scopus 로고
    • The influence of monovalent cation size on the stability of RNA tertiary structures
    • Lambert D., Leipply D., Shiman R., Draper D.E. The influence of monovalent cation size on the stability of RNA tertiary structures. J. Mol. Biol. 2009, 390:791-804.
    • (2009) J. Mol. Biol. , vol.390 , pp. 791-804
    • Lambert, D.1    Leipply, D.2    Shiman, R.3    Draper, D.E.4
  • 75
    • 0034622981 scopus 로고    scopus 로고
    • Stabilization of RNA tertiary structure by monovalent cations
    • Shiman R., Draper D.E. Stabilization of RNA tertiary structure by monovalent cations. J. Mol. Biol. 2000, 302:79-91.
    • (2000) J. Mol. Biol. , vol.302 , pp. 79-91
    • Shiman, R.1    Draper, D.E.2
  • 79
    • 79955604950 scopus 로고    scopus 로고
    • Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation
    • Blouin S., Chinnappan R., Lafontaine D.A. Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. Nucleic Acids Res. 2011, 39:3373-3387.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 3373-3387
    • Blouin, S.1    Chinnappan, R.2    Lafontaine, D.A.3
  • 81
    • 84857438025 scopus 로고    scopus 로고
    • An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches
    • Sherman E.M., Esquiaqui J., Elsayed G., Ye J.D. An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches. RNA 2012, 18:496-507.
    • (2012) RNA , vol.18 , pp. 496-507
    • Sherman, E.M.1    Esquiaqui, J.2    Elsayed, G.3    Ye, J.D.4
  • 82
    • 84856246110 scopus 로고    scopus 로고
    • Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches
    • Kladwang W., Chou F.C., Das R. Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches. J. Am. Chem. Soc. 2012, 134:1404-1407.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 1404-1407
    • Kladwang, W.1    Chou, F.C.2    Das, R.3
  • 83
    • 84872517135 scopus 로고    scopus 로고
    • Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches
    • Baird N.J., Ferre-D'Amare A.R. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 2013, 19:167-176.
    • (2013) RNA , vol.19 , pp. 167-176
    • Baird, N.J.1    Ferre-D'Amare, A.R.2
  • 86
    • 79851499341 scopus 로고    scopus 로고
    • Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms
    • Lemay J.F., Desnoyers G., Blouin S., Heppell B., Bastet L., St-Pierre P., Masse E., Lafontaine D.A. Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet. 2011, 7:e1001278.
    • (2011) PLoS Genet. , vol.7 , pp. e1001278
    • Lemay, J.F.1    Desnoyers, G.2    Blouin, S.3    Heppell, B.4    Bastet, L.5    St-Pierre, P.6    Masse, E.7    Lafontaine, D.A.8
  • 87
    • 34447548824 scopus 로고    scopus 로고
    • Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control
    • Rieder R., Lang K., Graber D., Micura R. Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. Chembiochem 2007, 8:896-902.
    • (2007) Chembiochem , vol.8 , pp. 896-902
    • Rieder, R.1    Lang, K.2    Graber, D.3    Micura, R.4
  • 88
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    • Wickiser J.K., Winkler W.C., Breaker R.R., Crothers D.M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 2005, 18:49-60.
    • (2005) Mol. Cell , vol.18 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 89
    • 0028020630 scopus 로고
    • Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate
    • McDowell J.C., Roberts J.W., Jin D.J., Gross C. Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science 1994, 266:822-825.
    • (1994) Science , vol.266 , pp. 822-825
    • McDowell, J.C.1    Roberts, J.W.2    Jin, D.J.3    Gross, C.4
  • 90
    • 84866340759 scopus 로고    scopus 로고
    • Insights into the regulatory landscape of the lysine riboswitch
    • Garst A.D., Porter E.B., Batey R.T. Insights into the regulatory landscape of the lysine riboswitch. J. Mol. Biol. 2012, 423:17-33.
    • (2012) J. Mol. Biol. , vol.423 , pp. 17-33
    • Garst, A.D.1    Porter, E.B.2    Batey, R.T.3
  • 91
    • 80053216036 scopus 로고    scopus 로고
    • Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism
    • Neupane K., Yu H., Foster D.A., Wang F., Woodside M.T. Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism. Nucleic Acids Res. 2011, 39:7677-7687.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 7677-7687
    • Neupane, K.1    Yu, H.2    Foster, D.A.3    Wang, F.4    Woodside, M.T.5
  • 92
    • 84877029646 scopus 로고    scopus 로고
    • RNA polymerase and the ribosome: the close relationship
    • McGary K., Nudler E. RNA polymerase and the ribosome: the close relationship. Curr. Opin. Microbiol. 2013, 16:112-117.
    • (2013) Curr. Opin. Microbiol. , vol.16 , pp. 112-117
    • McGary, K.1    Nudler, E.2
  • 93
    • 77954627972 scopus 로고    scopus 로고
    • Folding of a transcriptionally acting preQ1 riboswitch
    • Rieder U., Kreutz C., Micura R. Folding of a transcriptionally acting preQ1 riboswitch. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:10804-10809.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 10804-10809
    • Rieder, U.1    Kreutz, C.2    Micura, R.3
  • 94
    • 77954649566 scopus 로고    scopus 로고
    • The apo riboswitch as a molecular hydra
    • Wedekind J.E. The apo riboswitch as a molecular hydra. Structure 2010, 18:757-758.
    • (2010) Structure , vol.18 , pp. 757-758
    • Wedekind, J.E.1
  • 95
    • 35648974802 scopus 로고    scopus 로고
    • Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution
    • Buck J., Furtig B., Noeske J., Wohnert J., Schwalbe H. Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:15699-15704.
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 15699-15704
    • Buck, J.1    Furtig, B.2    Noeske, J.3    Wohnert, J.4    Schwalbe, H.5
  • 96
    • 36248984806 scopus 로고    scopus 로고
    • Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism
    • Ottink O.M., Rampersad S.M., Tessari M., Zaman G.J., Heus H.A., Wijmenga S.S. Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism. RNA 2007, 13:2202-2212.
    • (2007) RNA , vol.13 , pp. 2202-2212
    • Ottink, O.M.1    Rampersad, S.M.2    Tessari, M.3    Zaman, G.J.4    Heus, H.A.5    Wijmenga, S.S.6
  • 98
    • 70350149960 scopus 로고    scopus 로고
    • Sequence-dependent folding and unfolding of ligand-bound purine riboswitches
    • Prychyna O., Dahabieh M.S., Chao J., O'Neill M.A. Sequence-dependent folding and unfolding of ligand-bound purine riboswitches. Biopolymers 2009, 91:953-965.
    • (2009) Biopolymers , vol.91 , pp. 953-965
    • Prychyna, O.1    Dahabieh, M.S.2    Chao, J.3    O'Neill, M.A.4
  • 99
    • 84867629183 scopus 로고    scopus 로고
    • Direct observation of cotranscriptional folding in an adenine riboswitch
    • Frieda K.L., Block S.M. Direct observation of cotranscriptional folding in an adenine riboswitch. Science 2012, 338:397-400.
    • (2012) Science , vol.338 , pp. 397-400
    • Frieda, K.L.1    Block, S.M.2
  • 100
    • 38849204944 scopus 로고    scopus 로고
    • Direct observation of hierarchical folding in single riboswitch aptamers
    • Greenleaf W.J., Frieda K.L., Foster D.A., Woodside M.T., Block S.M. Direct observation of hierarchical folding in single riboswitch aptamers. Science 2008, 319:630-633.
    • (2008) Science , vol.319 , pp. 630-633
    • Greenleaf, W.J.1    Frieda, K.L.2    Foster, D.A.3    Woodside, M.T.4    Block, S.M.5
  • 101
    • 67650032475 scopus 로고    scopus 로고
    • Energy flow and long-range correlations in guanine-binding riboswitch: a nonequilibrium molecular dynamics study
    • Nguyen P.H., Derreumaux P., Stock G. Energy flow and long-range correlations in guanine-binding riboswitch: a nonequilibrium molecular dynamics study. J. Phys. Chem. B 2009, 113:9340-9347.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 9340-9347
    • Nguyen, P.H.1    Derreumaux, P.2    Stock, G.3
  • 102
    • 69049108817 scopus 로고    scopus 로고
    • Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
    • Villa A., Wohnert J., Stock G. Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res. 2009, 37:4774-4786.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 4774-4786
    • Villa, A.1    Wohnert, J.2    Stock, G.3
  • 103
    • 69049086655 scopus 로고    scopus 로고
    • MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch
    • Sharma M., Bulusu G., Mitra A. MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch. RNA 2009, 15:1673-1692.
    • (2009) RNA , vol.15 , pp. 1673-1692
    • Sharma, M.1    Bulusu, G.2    Mitra, A.3
  • 104
    • 80052240487 scopus 로고    scopus 로고
    • Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation
    • Gong Z., Zhao Y., Chen C., Xiao Y. Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation. J. Biomol. Struct. Dyn. 2011, 29:403-416.
    • (2011) J. Biomol. Struct. Dyn. , vol.29 , pp. 403-416
    • Gong, Z.1    Zhao, Y.2    Chen, C.3    Xiao, Y.4
  • 105
    • 77952700860 scopus 로고    scopus 로고
    • Real-time multidimensional NMR follows RNA folding with second resolution
    • Lee M.K., Gal M., Frydman L., Varani G. Real-time multidimensional NMR follows RNA folding with second resolution. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:9192-9197.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 9192-9197
    • Lee, M.K.1    Gal, M.2    Frydman, L.3    Varani, G.4
  • 106
    • 77649274141 scopus 로고    scopus 로고
    • Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch
    • Priyakumar U.D., MacKerell A.D. Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J. Mol. Biol. 2010, 396:1422-1438.
    • (2010) J. Mol. Biol. , vol.396 , pp. 1422-1438
    • Priyakumar, U.D.1    MacKerell, A.D.2
  • 108
    • 75449112058 scopus 로고    scopus 로고
    • Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in
    • Ditzler M.A., Otyepka M., Sponer J., Walter N.G. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc. Chem. Res. 2010, 43:40-47.
    • (2010) Acc. Chem. Res. , vol.43 , pp. 40-47
    • Ditzler, M.A.1    Otyepka, M.2    Sponer, J.3    Walter, N.G.4
  • 109
    • 33847318371 scopus 로고    scopus 로고
    • Molecular dynamics simulations of RNA: an in silico single molecule approach
    • McDowell S.E., Špačková N.a., Šponer J., Walter N.G. Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers 2007, 85:169-184.
    • (2007) Biopolymers , vol.85 , pp. 169-184
    • McDowell, S.E.1    Špačková, N.2    Šponer, J.3    Walter, N.G.4
  • 111
    • 46349083026 scopus 로고    scopus 로고
    • The distributions, mechanisms, and structures of metabolite-binding riboswitches
    • Barrick J.E., Breaker R.R. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 2007, 8:R239.
    • (2007) Genome Biol. , vol.8 , pp. R239
    • Barrick, J.E.1    Breaker, R.R.2
  • 113
    • 80053008165 scopus 로고    scopus 로고
    • Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing
    • Meyer M., Plass M., Perez-Valle J., Eyras E., Vilardell J. Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing. Mol. Cell 2011, 43:1033-1039.
    • (2011) Mol. Cell , vol.43 , pp. 1033-1039
    • Meyer, M.1    Plass, M.2    Perez-Valle, J.3    Eyras, E.4    Vilardell, J.5
  • 114
    • 0037031594 scopus 로고    scopus 로고
    • An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes
    • Johansson J., Mandin P., Renzoni A., Chiaruttini C., Springer M., Cossart P. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 2002, 110:551-561.
    • (2002) Cell , vol.110 , pp. 551-561
    • Johansson, J.1    Mandin, P.2    Renzoni, A.3    Chiaruttini, C.4    Springer, M.5    Cossart, P.6
  • 115
    • 0001641104 scopus 로고    scopus 로고
    • Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor
    • Morita M.T., Tanaka Y., Kodama T.S., Kyogoku Y., Yanagi H., Yura T. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Genes Dev. 1999, 13:655-665.
    • (1999) Genes Dev. , vol.13 , pp. 655-665
    • Morita, M.T.1    Tanaka, Y.2    Kodama, T.S.3    Kyogoku, Y.4    Yanagi, H.5    Yura, T.6
  • 117
    • 84880512394 scopus 로고    scopus 로고
    • Three-state mechanism couples ligand and temperature sensing in riboswitches
    • Reining A., Nozinovic S., Schlepckow K., Buhr F., Furtig B., Schwalbe H. Three-state mechanism couples ligand and temperature sensing in riboswitches. Nature 2013, 499:355-359.
    • (2013) Nature , vol.499 , pp. 355-359
    • Reining, A.1    Nozinovic, S.2    Schlepckow, K.3    Buhr, F.4    Furtig, B.5    Schwalbe, H.6
  • 118
    • 78149300889 scopus 로고    scopus 로고
    • Structural basis for recognition of S-adenosylhomocysteine by riboswitches
    • Edwards A.L., Reyes F.E., Heroux A., Batey R.T. Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA 2010, 16:2144-2155.
    • (2010) RNA , vol.16 , pp. 2144-2155
    • Edwards, A.L.1    Reyes, F.E.2    Heroux, A.3    Batey, R.T.4
  • 121
    • 84865297453 scopus 로고    scopus 로고
    • Synthetic biology with RNA: progress report
    • Benenson Y. Synthetic biology with RNA: progress report. Curr. Opin. Chem. Biol. 2012, 16:278-284.
    • (2012) Curr. Opin. Chem. Biol. , vol.16 , pp. 278-284
    • Benenson, Y.1
  • 123
    • 84863617223 scopus 로고    scopus 로고
    • Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators
    • Wittmann A., Suess B. Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett. 2012, 586:2076-2083.
    • (2012) FEBS Lett. , vol.586 , pp. 2076-2083
    • Wittmann, A.1    Suess, B.2
  • 124
    • 75749138167 scopus 로고    scopus 로고
    • Emerging applications of riboswitches in chemical biology
    • Topp S., Gallivan J.P. Emerging applications of riboswitches in chemical biology. ACS Chem. Biol. 2010, 5:139-148.
    • (2010) ACS Chem. Biol. , vol.5 , pp. 139-148
    • Topp, S.1    Gallivan, J.P.2
  • 127
    • 84882622399 scopus 로고    scopus 로고
    • Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices
    • Ceres P., Garst A.D., Marcano-Velazquez J.G., Batey R.T. Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth. Biol. 2013, 2:463-472.
    • (2013) ACS Synth. Biol. , vol.2 , pp. 463-472
    • Ceres, P.1    Garst, A.D.2    Marcano-Velazquez, J.G.3    Batey, R.T.4
  • 128
    • 80054074740 scopus 로고    scopus 로고
    • The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer
    • Trausch J.J., Ceres P., Reyes F.E., Batey R.T. The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure 2011, 19:1413-1423.
    • (2011) Structure , vol.19 , pp. 1413-1423
    • Trausch, J.J.1    Ceres, P.2    Reyes, F.E.3    Batey, R.T.4
  • 130
    • 84890327325 scopus 로고    scopus 로고
    • Engineering modular 'ON' RNA switches using biological components
    • Ceres P., Trausch J.J., Batey R.T. Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res. 2013, 41:10449-10461.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 10449-10461
    • Ceres, P.1    Trausch, J.J.2    Batey, R.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.