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Volumn 39, Issue 17, 2011, Pages 7677-7687

Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; BACTERIAL RNA;

EID: 80053216036     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr305     Document Type: Article
Times cited : (104)

References (49)
  • 1
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolite-binding riboswitches
    • Roth, A. and Breaker, R.R. (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem., 78, 305-334.
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 305-334
    • Roth, A.1    Breaker, R.R.2
  • 2
    • 34247111235 scopus 로고    scopus 로고
    • The intricate world of riboswitches
    • DOI 10.1016/j.mib.2007.03.006, PII S1369527407000239, Cell Regulation (RNA Special Issue)
    • Coppins, R.L., Hall, K.B. and Groisman, E.A. (2007) The intricate world of riboswitches. Curr. Opin. Microbiol., 10, 176-181. (Pubitemid 46590046)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.2 , pp. 176-181
    • Coppins, R.L.1    Hall, K.B.2    Groisman, E.A.3
  • 3
    • 77149165421 scopus 로고    scopus 로고
    • Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
    • Baird, N.J. and Ferré-D'Amaré, A.R. (2010) Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA, 16, 598-609.
    • (2010) RNA , vol.16 , pp. 598-609
    • Baird, N.J.1    Ferré-D'Amaré, A.R.2
  • 4
    • 38849103659 scopus 로고    scopus 로고
    • Purine sensing by riboswitches
    • DOI 10.1042/BC20070088
    • Kim, J.N. and Breaker, R.R. (2008) Purine sensing by riboswitches. Biol. Cell., 100, 1-11. (Pubitemid 351201429)
    • (2008) Biology of the Cell , vol.100 , Issue.1 , pp. 1-11
    • Kim, J.N.1    Breaker, R.R.2
  • 5
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • DOI 10.1016/S0092-8674(03)00391-X
    • Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C. and Breaker, R.R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell, 113, 577-586. (Pubitemid 36694183)
    • (2003) Cell , vol.113 , Issue.5 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 6
    • 0842334528 scopus 로고    scopus 로고
    • Adenine riboswitches and gene activation by disruption of a transcription terminator
    • DOI 10.1038/nsmb710
    • Mandal, M. and Breaker, R.R. (2004) Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol., 11, 29-35. (Pubitemid 38173438)
    • (2004) Nature Structural and Molecular Biology , vol.11 , Issue.1 , pp. 29-35
    • Mandal, M.1    Breaker, R.R.2
  • 8
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • DOI 10.1038/nature03037
    • Batey, R.T., Gilbert, S.D. and Montange, R.K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415. (Pubitemid 39551677)
    • (2004) Nature , vol.432 , Issue.7015 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 9
    • 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., Massé, E. and Lafontaine, D.A. (2011) Comparative study between transcriptionally-and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet., 7, e1001278.
    • (2011) PLoS Genet. , vol.7
    • Lemay, J.F.1    Desnoyers, G.2    Blouin, S.3    Heppell, B.4    Bastet, L.5    St-Pierre, P.6    Massé, E.7    Lafontaine, D.A.8
  • 11
    • 33646768226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
    • DOI 10.1016/j.jmb.2006.04.003, PII S0022283606004517
    • Gilbert, S.D., Stoddard, C.D., Wise, S.J. and Batey, R.T. (2006) Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J. Mol. Biol., 359, 754-768. (Pubitemid 43767264)
    • (2006) Journal of Molecular Biology , vol.359 , Issue.3 , pp. 754-768
    • Gilbert, S.D.1    Stoddard, C.D.2    Wise, S.J.3    Batey, R.T.4
  • 12
    • 34447548824 scopus 로고    scopus 로고
    • Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control
    • DOI 10.1002/cbic.200700057
    • Rieder, R., Lang, K., Graber, D. and Micura, R. (2007) Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. ChemBioChem, 8, 896-902. (Pubitemid 47194838)
    • (2007) ChemBioChem , vol.8 , Issue.8 , pp. 896-902
    • Rieder, R.1    Lang, K.2    Graber, D.3    Micura, R.4
  • 14
    • 77955081034 scopus 로고    scopus 로고
    • Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain
    • Buck, J., Noeske, J., Wöhnert, J. and Schwalbe, H. (2010) Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res., 38, 4143-4153.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4143-4153
    • Buck, J.1    Noeske, J.2    Wöhnert, J.3    Schwalbe, H.4
  • 15
    • 38849204944 scopus 로고    scopus 로고
    • Direct observation of hierarchical folding in single riboswitch aptamers
    • DOI 10.1126/science.1151298
    • Greenleaf, W.J., Frieda, K.L., Foster, D.A.N., Woodside, M.T. and Block, S.M. (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science, 319, 630-633. (Pubitemid 351197067)
    • (2008) Science , vol.319 , Issue.5863 , pp. 630-633
    • Greenleaf, W.J.1    Frieda, K.L.2    Foster, D.A.N.3    Woodside, M.T.4    Block, S.M.5
  • 16
    • 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
    • DOI 10.1093/nar/gkl1094
    • Noeske, J., Buck, J., Fürtig, B., Nasiri, H.R., Schwalbe, H. and Wöhnert, J. (2007) Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res., 35, 572-583. (Pubitemid 46232073)
    • (2007) Nucleic Acids Research , vol.35 , Issue.2 , pp. 572-583
    • Noeske, J.1    Buck, J.2    Furtig, B.3    Nasiri, H.R.4    Schwalbe, H.5    Wohnert, J.6
  • 17
    • 36248984806 scopus 로고    scopus 로고
    • Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined-induced fit mechanism
    • DOI 10.1261/rna.635307
    • Ottink, O.M., Rampersad, S.M., Tessari, M., Zaman, G.J.R., Heus, H.A. and Wijmenga, S.S. (2007) Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined-induced fit mechanism. RNA, 13, 2202-2212. (Pubitemid 350127561)
    • (2007) RNA , vol.13 , Issue.12 , pp. 2202-2212
    • Ottink, O.M.1    Rampersad, S.M.2    Tessari, M.3    Zaman, G.J.R.4    Heus, H.A.5    Wijmenga, S.S.6
  • 18
    • 41649108293 scopus 로고    scopus 로고
    • Ligand-dependent folding of the three-way junction in the purine riboswitch
    • DOI 10.1261/rna.736908
    • Stoddard, C.D., Gilbert, S.D. and Batey, R.T. (2008) Ligand-dependent folding of the three-way junction in the purine riboswitch. RNA, 14, 675-684. (Pubitemid 351480880)
    • (2008) RNA , vol.14 , Issue.4 , pp. 675-684
    • Stoddard, C.D.1    Gilbert, S.D.2    Batey, R.T.3
  • 19
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • DOI 10.1021/bi051008u
    • Wickiser, J.K., Cheah, M.T., Breaker, R.B. and Crothers, D.M. (2005) The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry, 44, 13404-13414. (Pubitemid 41429463)
    • (2005) Biochemistry , vol.44 , Issue.40 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 20
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    • DOI 10.1016/j.molcel.2005.02.032
    • Wickiser, J.K., Winkler, W.C., Breaker, R.R. and Crothers, D.M. (2005) The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell, 18, 49-60. (Pubitemid 40444647)
    • (2005) Molecular Cell , vol.18 , Issue.1 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 21
    • 77954627972 scopus 로고    scopus 로고
    • Folding of a transcriptionally acting PreQ1 riboswitch
    • Rieder, U., Kreutz, C. and Micura, R. (2010) Folding of a transcriptionally acting PreQ1 riboswitch. Proc. Natl Acad. Sci. USA, 107, 10804-10809.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 10804-10809
    • Rieder, U.1    Kreutz, C.2    Micura, R.3
  • 22
    • 78049276834 scopus 로고    scopus 로고
    • Ribozymes and riboswitches: Modulation of RNA function by small molecules
    • Zhang, J., Lau, M.W. and Ferré-D'Amaré, A.R. (2010) Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules. Biochemistry, 49, 9123-9131.
    • (2010) Biochemistry , vol.49 , pp. 9123-9131
    • Zhang, J.1    Lau, M.W.2    Ferré-D'Amaré, A.R.3
  • 25
    • 0023022499 scopus 로고
    • Analysis of enzymatically amplified β-globin and HLA-DQα DNA with allele-specific oligonucleotide probes
    • DOI 10.1038/324163a0
    • Saiki, R.K., Bugawan, T.L., Horn, G.T., Mullis, K.B. and Erlich, H.A. (1986) Analysis of enzymatically amplified beta-globin and HLA-DQ alpha DNA with allele-specific oligonucleotide probes. Nature, 324, 163-166. (Pubitemid 17180630)
    • (1986) Nature , vol.324 , Issue.6093 , pp. 163-166
    • Saiki, R.K.1    Bugawan, T.L.2    Horn, G.T.3
  • 28
    • 0030024985 scopus 로고    scopus 로고
    • Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
    • Smith, S.B., Cui, Y. and Bustamante, C. (1996) Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271, 795-799.
    • (1996) Science , vol.271 , pp. 795-799
    • Smith, S.B.1    Cui, Y.2    Bustamante, C.3
  • 29
    • 0035957720 scopus 로고    scopus 로고
    • Reversible unfolding of single RNA molecules by mechanical force
    • DOI 10.1126/science.1058498
    • Liphardt, J., Onoa, B., Smith, S.B., Tinoco, I.J. and Bustamante, C. (2001) Reversible unfolding of single RNA molecules by mechanical force. Science, 292, 733-737. (Pubitemid 32385545)
    • (2001) Science , vol.292 , Issue.5517 , pp. 733-737
    • Liphardt, J.1    Onoa, B.2    Smith, S.B.3    Tinoco Jr., I.4    Bustamante, C.5
  • 31
    • 19644366142 scopus 로고    scopus 로고
    • Elastic properties of a single-stranded charged homopolymeric ribonucleotide
    • Seol, Y., Skinner, G.M. and Visscher, K. (2004) Elastic properties of a single-stranded charged homopolymeric ribonucleotide. Phys. Rev. Lett., 93, 118102-118105.
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 118102-118105
    • Seol, Y.1    Skinner, G.M.2    Visscher, K.3
  • 33
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. (1997) Nonequilibrium equality for free energy differences. Phys. Rev. Lett., 78, 2690-2693. (Pubitemid 127655287)
    • (1997) Physical Review Letters , vol.78 , Issue.14 , pp. 2690-2693
    • Jarzynski, C.1
  • 34
    • 35648974802 scopus 로고    scopus 로고
    • Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution
    • Buck, J., Fürtig, B., Noeske, J., Wöhnert, J. and Schwalbe, H. (2007) Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution. Proc. Natl Acad. Sci. USA, 104, 15699-16704.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 15699-16704
    • Buck, J.1    Fürtig, B.2    Noeske, J.3    Wöhnert, J.4    Schwalbe, H.5
  • 35
    • 33645004171 scopus 로고    scopus 로고
    • Intrinsic rates and activation free energies from single-molecule pulling experiments
    • Dudko, O.K., Hummer, G. and Szabo, A. (2006) Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys. Rev. Lett., 96, 108101-108104.
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 108101-108104
    • Dudko, O.K.1    Hummer, G.2    Szabo, A.3
  • 36
    • 57349124448 scopus 로고    scopus 로고
    • Theory analysis, and interpretation of single-molecule force spectroscopy experiments
    • Dudko, O.K., Hummer, G. and Szabo, A. (2008) Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc. Natl. Acad. Sci. USA, 105, 15755-15760.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 15755-15760
    • Dudko, O.K.1    Hummer, G.2    Szabo, A.3
  • 37
    • 33750970551 scopus 로고    scopus 로고
    • Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
    • DOI 10.1126/science.1133601
    • Woodside, M.T., Anthony, P.C., Behnke-Parks, W.M., Larizadeh, K., Herschlag, D. and Block, S.M. (2006) Direct measurement of the full sequence-dependent folding landscape of a nucleic acid. Science, 314, 1001-1004. (Pubitemid 44749947)
    • (2006) Science , vol.314 , Issue.5801 , pp. 1001-1004
    • Woodside, M.T.1    Anthony, P.C.2    Behnke-Parks, W.M.3    Larizadeh, K.4    Herschlag, D.5    Block, S.M.6
  • 38
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • DOI 10.1093/nar/gkg595
    • Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415. (Pubitemid 37442169)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 39
    • 0042622372 scopus 로고    scopus 로고
    • RNAsoft: A suite of RNA secondary structure prediction and design software tools
    • DOI 10.1093/nar/gkg612
    • Andronescu, M., Aguirre-Hernandez, R., Condon, A. and Hoos, H.H. (2003) RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res., 31, 3416-3422. (Pubitemid 37442170)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3416-3422
    • Andronescu, M.1    Aguirre-Hernandez, R.2    Condon, A.3    Hoos, H.H.4
  • 40
    • 38449108345 scopus 로고    scopus 로고
    • RNA misfolding and the action of chaperones
    • DOI 10.2741/2557
    • Russell, R. (2008) RNA misfolding and the action of chaperones. Front Biosci, 13, 1-20. (Pubitemid 351594760)
    • (2008) Frontiers in Bioscience , vol.13 , Issue.1 , pp. 1-20
    • Russell, R.1
  • 43
    • 0026566314 scopus 로고
    • Parameters affecting transcription termination by Escherichia coli RNA polymerase: I. Analysis of 13 rho-independent terminators
    • Reynolds, R., Bermú dez-Cruz, R.M. and Chamberlin, M.J. (1992) Parameters affecting transcription termination by Escherichia coli RNA polymerase: I. Analysis of 13 rho-independent terminators. J. Mol. Biol., 224, 31-51.
    • (1992) J. Mol. Biol. , vol.224 , pp. 31-51
    • Reynolds, R.1    Bermúdez-Cruz, R.M.2    Chamberlin, M.J.3
  • 44
    • 29144526713 scopus 로고    scopus 로고
    • Determination of the termination efficiency of the transcription terminator using different fluorescent profiles in green fluorescent protein mutants
    • DOI 10.2116/analsci.21.1479
    • Nojima, T., Lin, A.C., Fujii, T. and Endo, I. (2005) Determination of the termination efficiency of the transcription terminator using different fluorescent profiles in green fluorescent protein mutants. Anal. Sci., 21, 1479-1481. (Pubitemid 41797872)
    • (2005) Analytical Sciences , vol.21 , Issue.12 , pp. 1479-1481
    • Nojima, T.1    Lin, A.C.2    Fujii, T.3    Endo, I.4
  • 45
    • 54849437727 scopus 로고    scopus 로고
    • Relative stability of helices determines the folding landscape of adenine riboswitch aptamers
    • Lin, J.-C. and Thirumalai, D. (2008) Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J. Am. Chem. Soc., 130, 14080-14081.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 14080-14081
    • Lin, J.-C.1    Thirumalai, D.2
  • 46
    • 77951589688 scopus 로고    scopus 로고
    • Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    • Proshkin, S., Rahmouni, A.R., Mironov, A. and Nudler, E. (2010) Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science, 328, 504-508.
    • (2010) Science , vol.328 , pp. 504-508
    • Proshkin, S.1    Rahmouni, A.R.2    Mironov, A.3    Nudler, E.4
  • 47
    • 0028227702 scopus 로고
    • The RNA chain elongation rate in Escherichia coli depends on the growth rate
    • Vogel, U. and Jensen, K.F. (1994) The RNA chain elongation rate in Excherichia coli depends on the growth rate. J. Bacteriol., 176, 2807-2813. (Pubitemid 24152923)
    • (1994) Journal of Bacteriology , vol.176 , Issue.10 , pp. 2807-2813
    • Vogel, U.1    Jensen, K.F.2
  • 48
    • 0028094403 scopus 로고
    • Footprinting mRNA-ribosome complexes with chemical probes
    • Hü ttenhofer, A. and Noller, H.F. (1994) Footprinting mRNA-ribosome complexes with chemical probes. EMBO J., 13, 3892-3901.
    • (1994) EMBO J. , vol.13 , pp. 3892-3901
    • Hüttenhofer, A.1    Noller, H.F.2
  • 49
    • 0035958587 scopus 로고    scopus 로고
    • The path of messenger RNA through the ribosome
    • DOI 10.1016/S0092-8674(01)00435-4
    • Yusupova, G.Z., Yusupov, M.M., Cate, J.H.D. and Noller, H.F. (2001) The path of messenger RNA through the ribosome. Cell, 106, 233-241. (Pubitemid 32772633)
    • (2001) Cell , vol.106 , Issue.2 , pp. 233-241
    • Yusupova, G.Zh.1    Yusupov, M.M.2    Cate, J.H.D.3    Noller, H.F.4


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