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Volumn 16, Issue 4, 2010, Pages 708-719

Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

Author keywords

Riboswitches; RNA aptamers; RNA folding; Small angle X ray scattering; Specific ion binding

Indexed keywords

APTAMER; CALCIUM; DIVALENT CATION; GLYCINE; HYDROXYL RADICAL; MAGNESIUM; MANGANESE; MONOVALENT CATION;

EID: 77950292093     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1985110     Document Type: Article
Times cited : (53)

References (83)
  • 1
    • 74649084566 scopus 로고    scopus 로고
    • The ligand-free state of the TPP riboswitch: A partially folded RNA structure
    • Ali M, Lipfert J, Seifert S, Herschlag D, Doniach S. 2009. The ligand-free state of the TPP riboswitch: A partially folded RNA structure. J Mol Biol 396: 153-165.
    • (2009) J Mol Biol , vol.396 , pp. 153-165
    • Ali, M.1    Lipfert, J.2    Seifert, S.3    Herschlag, D.4    Doniach, S.5
  • 2
    • 27944484382 scopus 로고    scopus 로고
    • Incorporation of excluded-volume correlations into Poisson-Boltzmann theory
    • doi: 10.1103/PhysRevE. 71.061106
    • Antypov D, Barbosa MC, Holm C. 2005. Incorporation of excluded-volume correlations into Poisson-Boltzmann theory. Phys Rev E Stat Nonlin Soft Matter Phys 71: 061106. doi: 10.1103/PhysRevE. 71.061106.
    • (2005) Phys Rev e Stat Nonlin Soft Matter Phys , vol.71 , pp. 061106
    • Antypov, D.1    Barbosa, M.C.2    Holm, C.3
  • 4
    • 51949119253 scopus 로고    scopus 로고
    • Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble
    • Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, Doniach S. 2008. Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. J Am Chem Soc 130: 12334-12341.
    • (2008) J Am Chem Soc , vol.130 , pp. 12334-12341
    • Bai, Y.1    Chu, V.B.2    Lipfert, J.3    Pande, V.S.4    Herschlag, D.5    Doniach, S.6
  • 5
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: Application to microtubules and the ribosome
    • Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci 98: 10037-10041.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5
  • 6
    • 0043163762 scopus 로고    scopus 로고
    • Microenvironment analysis and identification of magnesium binding sites in RNA
    • Banatao DR, Altman RB, Klein TE. 2003. Microenvironment analysis and identification of magnesium binding sites in RNA. Nucleic Acids Res 31: 4450-4460.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4450-4460
    • Banatao, D.R.1    Altman, R.B.2    Klein, T.E.3
  • 8
    • 0036816641 scopus 로고    scopus 로고
    • Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical 'footprinting'
    • Brenowitz M, Chance MR, Dhavan G, Takamoto K. 2002. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical 'footprinting'. Curr Opin Struct Biol 12: 648-653.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 648-653
    • Brenowitz, M.1    Chance, M.R.2    Dhavan, G.3    Takamoto, K.4
  • 9
    • 0031567680 scopus 로고    scopus 로고
    • Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure
    • Bukhman YV, Draper DE. 1997. Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure. J Mol Biol 273: 1020-1031.
    • (1997) J Mol Biol , vol.273 , pp. 1020-1031
    • Bukhman, Y.V.1    Draper, D.E.2
  • 10
    • 0035477789 scopus 로고    scopus 로고
    • Modeling ion binding to AA platform motifs in RNA: A continuum solvent study including conformational adaptation
    • Burkhardt C, Zacharias M. 2001. Modeling ion binding to AA platform motifs in RNA: A continuum solvent study including conformational adaptation. Nucleic Acids Res 29: 3910-3918.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3910-3918
    • Burkhardt, C.1    Zacharias, M.2
  • 11
    • 0030587890 scopus 로고    scopus 로고
    • Metal-binding sites in the major groove of a large ribozyme domain
    • Cate JH, Doudna JA. 1996. Metal-binding sites in the major groove of a large ribozyme domain. Structure 4: 1221-1229.
    • (1996) Structure , vol.4 , pp. 1221-1229
    • Cate, J.H.1    Doudna, J.A.2
  • 12
    • 0030929889 scopus 로고    scopus 로고
    • A magnesium ion core at the heart of a ribozyme domain
    • Cate JH, Hanna RL, Doudna JA. 1997. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol 4: 553-558.
    • (1997) Nat Struct Biol , vol.4 , pp. 553-558
    • Cate, J.H.1    Hanna, R.L.2    Doudna, J.A.3
  • 13
    • 0025023607 scopus 로고
    • Iron(II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- And double-stranded forms
    • Celander DW, Cech TR. 1990. Iron(II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms. Biochemistry 29: 1355-1361.
    • (1990) Biochemistry , vol.29 , pp. 1355-1361
    • Celander, D.W.1    Cech, T.R.2
  • 14
    • 0032707625 scopus 로고    scopus 로고
    • Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function
    • Chin K, Sharp KA, Honig B, Pyle AM. 1999. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function. Nat Struct Biol 6: 1055-1061.
    • (1999) Nat Struct Biol , vol.6 , pp. 1055-1061
    • Chin, K.1    Sharp, K.A.2    Honig, B.3    Pyle, A.M.4
  • 15
    • 0027473887 scopus 로고
    • Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme
    • Chowrira BM, Berzal-Herranz A, Burke JM. 1993. Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme. Biochemistry 32: 1088-1095.
    • (1993) Biochemistry , vol.32 , pp. 1088-1095
    • Chowrira, B.M.1    Berzal-Herranz, A.2    Burke, J.M.3
  • 16
    • 36048952831 scopus 로고    scopus 로고
    • Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory
    • Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. 2007. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophys J 93: 3202-3209.
    • (2007) Biophys J , vol.93 , pp. 3202-3209
    • Chu, V.B.1    Bai, Y.2    Lipfert, J.3    Herschlag, D.4    Doniach, S.5
  • 17
  • 18
    • 73249135897 scopus 로고    scopus 로고
    • Do conformational biases of simple helical junctions influence RNA folding stability and specificity?
    • Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D. 2009. Do conformational biases of simple helical junctions influence RNA folding stability and specificity? RNA 15: 2195-2205.
    • (2009) RNA , vol.15 , pp. 2195-2205
    • Chu, V.B.1    Lipfert, J.2    Bai, Y.3    Pande, V.S.4    Doniach, S.5    Herschlag, D.6
  • 22
    • 0025998488 scopus 로고
    • Role of divalent metal ions in the hammerhead RNA cleavage reaction
    • Dahm SC, Uhlenbeck OC. 1991. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30: 9464-9469.
    • (1991) Biochemistry , vol.30 , pp. 9464-9469
    • Dahm, S.C.1    Uhlenbeck, O.C.2
  • 25
    • 13944278373 scopus 로고    scopus 로고
    • SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. 2005a. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11: 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
  • 27
    • 0038170015 scopus 로고    scopus 로고
    • Metal ion binding to catalytic RNA molecules
    • DeRose VJ. 2003. Metal ion binding to catalytic RNA molecules. Curr Opin Struct Biol 13: 317-324.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 317-324
    • Derose, V.J.1
  • 28
    • 1242274330 scopus 로고    scopus 로고
    • A guide to ions and RNA structure
    • Draper DE. 2004. A guide to ions and RNA structure. RNA 10: 335-343.
    • (2004) RNA , vol.10 , pp. 335-343
    • Draper, D.E.1
  • 29
    • 58749105663 scopus 로고    scopus 로고
    • RNA folding: Thermodynamic and molecular descriptions of the roles of ions
    • Draper DE. 2008. RNA folding: Thermodynamic and molecular descriptions of the roles of ions. Biophys J 95: 5489-5495.
    • (2008) Biophys J , vol.95 , pp. 5489-5495
    • Draper, D.E.1
  • 32
    • 0038719800 scopus 로고    scopus 로고
    • A crystallographic study of the binding of 13 metal ions to two related RNA duplexes
    • Ennifar E, Walter P, Dumas P. 2003. A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res 31: 2671-2682.
    • (2003) Nucleic Acids Res , vol.31 , pp. 2671-2682
    • Ennifar, E.1    Walter, P.2    Dumas, P.3
  • 33
    • 33749032381 scopus 로고    scopus 로고
    • 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures
    • 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc Natl Acad Sci 103: 14003-14008.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 14003-14008
    • Grilley, D.1    Soto, A.M.2    Draper, D.E.3
  • 34
    • 38949141177 scopus 로고    scopus 로고
    • Continuum molecular electrostatics, salt effects, and counterion binding - a review of the Poisson-Boltzmann theory and its modifications
    • Grochowski P, Trylska J. 2008. Continuum molecular electrostatics, salt effects, and counterion binding - a review of the Poisson-Boltzmann theory and its modifications. Biopolymers 89: 93-113.
    • (2008) Biopolymers , vol.89 , pp. 93-113
    • Grochowski, P.1    Trylska, J.2
  • 35
    • 0024976556 scopus 로고
    • Metal ion requirements for sequencespecific endoribonuclease activity of the Tetrahymena ribozyme
    • Grosshans CA, Cech TR. 1989. Metal ion requirements for sequencespecific endoribonuclease activity of the Tetrahymena ribozyme. Biochemistry 28: 6888-6894.
    • (1989) Biochemistry , vol.28 , pp. 6888-6894
    • Grosshans, C.A.1    Cech, T.R.2
  • 36
    • 0022530665 scopus 로고
    • Metal ion requirements and other aspects of the reaction catalyzed by M1 RNA, the RNA subunit of ribonuclease P from Escherichia coli
    • Guerrier-Takada C, Haydock K, Allen L, Altman S. 1986. Metal ion requirements and other aspects of the reaction catalyzed by M1 RNA, the RNA subunit of ribonuclease P from Escherichia coli. Biochemistry 25: 1509-1515.
    • (1986) Biochemistry , vol.25 , pp. 1509-1515
    • Guerrier-Takada, C.1    Haydock, K.2    Allen, L.3    Altman, S.4
  • 37
    • 0003043542 scopus 로고
    • The possible effects of the aggregation of the molecules of haemoglobin on its oxygen dissociation curve
    • Hill AV. 1910. The possible effects of the aggregation of the molecules of haemoglobin on its oxygen dissociation curve. J Physiol 40: 4-7.
    • (1910) J Physiol , vol.40 , pp. 4-7
    • Hill, A.V.1
  • 38
    • 0032559057 scopus 로고    scopus 로고
    • 2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity
    • 2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity. Biochemistry 37: 18094-18101.
    • (1998) Biochemistry , vol.37 , pp. 18094-18101
    • Horton, T.E.1    Clardy, D.R.2    Derose, V.J.3
  • 39
    • 33748325570 scopus 로고    scopus 로고
    • Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
    • Klein DJ, Ferré-D'Amaré AR. 2006. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313: 1752-1756.
    • (2006) Science , vol.313 , pp. 1752-1756
    • Klein, D.J.1    Ferré-D'Amaré, A.R.2
  • 40
    • 0035124442 scopus 로고    scopus 로고
    • Automated matching of high- and lowresolution structural models
    • Kozin MB, Svergun DI. 2001. Automated matching of high- and lowresolution structural models. J Appl Crystallogr 34: 33-41.
    • (2001) J Appl Crystallogr , vol.34 , pp. 33-41
    • Kozin, M.B.1    Svergun, D.I.2
  • 41
    • 71449123530 scopus 로고    scopus 로고
    • Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
    • Kulshina N, Baird NJ, Ferré-D'Amaré AR. 2009. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol 16: 1212-1217.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 1212-1217
    • Kulshina, N.1    Baird, N.J.2    Ferré-D'Amaré, A.R.3
  • 42
    • 38049025288 scopus 로고    scopus 로고
    • Chemical basis of glycine riboswitch cooperativity
    • Kwon M, Strobel SA. 2008. Chemical basis of glycine riboswitch cooperativity. RNA 14: 25-34.
    • (2008) RNA , vol.14 , pp. 25-34
    • Kwon, M.1    Strobel, S.A.2
  • 43
    • 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 DE. 2009. The influence of monovalent cation size on the stability of RNA tertiary structures. J Mol Biol 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
  • 44
    • 0024359787 scopus 로고
    • Defining the inside and outside of a catalytic RNA molecule
    • Latham JA, Cech TR. 1989. Defining the inside and outside of a catalytic RNA molecule. Science 245: 276-282.
    • (1989) Science , vol.245 , pp. 276-282
    • Latham, J.A.1    Cech, T.R.2
  • 48
    • 34249894142 scopus 로고    scopus 로고
    • Small-angle X-ray scattering from RNA, proteins, and protein complexes
    • Lipfert J, Doniach S. 2007. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36: 307-327.
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 307-327
    • Lipfert, J.1    Doniach, S.2
  • 49
    • 33646418410 scopus 로고    scopus 로고
    • Sample holder for small-angle x-ray scattering static and flow cell measurements
    • doi: 10.1063/1.2194484
    • Lipfert J, Millett IS, Seifert S, Doniach S. 2006. Sample holder for small-angle x-ray scattering static and flow cell measurements. Rev Sci Instrum 77: 046108. doi: 10.1063/1.2194484.
    • (2006) Rev Sci Instrum , vol.77 , pp. 046108
    • Lipfert, J.1    Millett, I.S.2    Seifert, S.3    Doniach, S.4
  • 50
    • 34248393495 scopus 로고    scopus 로고
    • Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling
    • Lipfert J, Chu VB, Bai Y, Herschlag D, Doniach S. 2007a. Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling. J Appl Crystallogr 40: S229-S234.
    • (2007) J Appl Crystallogr , vol.40
    • Lipfert, J.1    Chu, V.B.2    Bai, Y.3    Herschlag, D.4    Doniach, S.5
  • 51
    • 33845971464 scopus 로고    scopus 로고
    • Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae
    • Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. 2007b. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol 365: 1393-1406.
    • (2007) J Mol Biol , vol.365 , pp. 1393-1406
    • Lipfert, J.1    Das, R.2    Chu, V.B.3    Kudaravalli, M.4    Boyd, N.5    Herschlag, D.6    Doniach, S.7
  • 52
    • 50649108803 scopus 로고    scopus 로고
    • The complete VS ribozyme in solution studied by small-angle X-ray scattering
    • Lipfert J, Ouellet J, Norman DG, Doniach S, Lilley DM. 2008. The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure 16: 1357-1367.
    • (2008) Structure , vol.16 , pp. 1357-1367
    • Lipfert, J.1    Ouellet, J.2    Norman, D.G.3    Doniach, S.4    Lilley, D.M.5
  • 53
    • 65649141589 scopus 로고    scopus 로고
    • Riboswitch conformations revealed by small-angle X-ray scattering
    • Lipfert J, Herschlag D, Doniach S. 2009. Riboswitch conformations revealed by small-angle X-ray scattering. Methods Mol Biol 540: 141-159.
    • (2009) Methods Mol Biol , vol.540 , pp. 141-159
    • Lipfert, J.1    Herschlag, D.2    Doniach, S.3
  • 56
    • 0033579408 scopus 로고    scopus 로고
    • 2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory
    • 2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory. J Mol Biol 294: 1135-1147.
    • (1999) J Mol Biol , vol.294 , pp. 1135-1147
    • Misra, V.K.1    Draper, D.E.2
  • 57
    • 0034625314 scopus 로고    scopus 로고
    • 2+ binding to tRNA revisited: The nonlinear Poisson-Boltzmann model
    • 2+ binding to tRNA revisited: The nonlinear Poisson-Boltzmann model. J Mol Biol 299: 813-825.
    • (2000) J Mol Biol , vol.299 , pp. 813-825
    • Misra, V.K.1    Draper, D.E.2
  • 59
    • 0036295964 scopus 로고    scopus 로고
    • The linkage between magnesium binding and RNA folding
    • Misra VK, Draper DE. 2002. The linkage between magnesium binding and RNA folding. J Mol Biol 317: 507-521.
    • (2002) J Mol Biol , vol.317 , pp. 507-521
    • Misra, V.K.1    Draper, D.E.2
  • 60
    • 0037452909 scopus 로고    scopus 로고
    • Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism
    • Nakano S, Cerrone AL, Bevilacqua PC. 2003. Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry 42: 2982-2994.
    • (2003) Biochemistry , vol.42 , pp. 2982-2994
    • Nakano, S.1    Cerrone, A.L.2    Bevilacqua, P.C.3
  • 61
    • 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 HR, Schwalbe H, Wohnert J. 2007a. 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.
    • (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
  • 62
    • 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. 2007b. Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain. Nucleic Acids Res 35: 5262-5273.
    • (2007) Nucleic Acids Res , vol.35 , pp. 5262-5273
    • Noeske, J.1    Schwalbe, H.2    Wohnert, J.3
  • 63
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler E, Mironov AS. 2004. The riboswitch control of bacterial metabolism. Trends Biochem Sci 29: 11-17.
    • (2004) Trends Biochem Sci , vol.29 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 64
    • 43249119217 scopus 로고    scopus 로고
    • Direct measurement of tertiary contact cooperativity in RNA folding
    • Sattin BD, Zhao W, Travers K, Chu S, Herschlag D. 2008. Direct measurement of tertiary contact cooperativity in RNA folding. J Am Chem Soc 130: 6085-6087.
    • (2008) J Am Chem Soc , vol.130 , pp. 6085-6087
    • Sattin, B.D.1    Zhao, W.2    Travers, K.3    Chu, S.4    Herschlag, D.5
  • 65
    • 34247242053 scopus 로고    scopus 로고
    • Structures of RNA switches: Insight into molecular recognition and tertiary structure
    • Schwalbe H, Buck J, Furtig B, Noeske J, Wohnert J. 2007. Structures of RNA switches: Insight into molecular recognition and tertiary structure. Angew Chem Int Ed 46: 1212-1219.
    • (2007) Angew Chem Int Ed , vol.46 , pp. 1212-1219
    • Schwalbe, H.1    Buck, J.2    Furtig, B.3    Noeske, J.4    Wohnert, J.5
  • 66
    • 33745635350 scopus 로고    scopus 로고
    • Structural basis for gene regulation by a thiamine pyrophosphatesensing riboswitch
    • Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. 2006. Structural basis for gene regulation by a thiamine pyrophosphatesensing riboswitch. Nature 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
  • 68
    • 0038508653 scopus 로고    scopus 로고
    • RNA folding: Models and perspectives
    • Sosnick TR, Pan T. 2003. RNA folding: Models and perspectives. Curr Opin Struct Biol 13: 309-316.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 309-316
    • Sosnick, T.R.1    Pan, T.2
  • 70
    • 0033001996 scopus 로고    scopus 로고
    • Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
    • Svergun DI. 1999. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76: 2879-2886.
    • (1999) Biophys J , vol.76 , pp. 2879-2886
    • Svergun, D.I.1
  • 71
    • 4344590128 scopus 로고    scopus 로고
    • Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions
    • Takamoto K, Chance MR, Brenowitz M. 2004a. Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions. Nucleic Acids Res 32: E119.
    • (2004) Nucleic Acids Res , vol.32
    • Takamoto, K.1    Chance, M.R.2    Brenowitz, M.3
  • 72
    • 6344242969 scopus 로고    scopus 로고
    • Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations
    • Takamoto K, Das R, He Q, Doniach S, Brenowitz M, Herschlag D, Chance MR. 2004b. Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J Mol Biol 343: 1195-1206.
    • (2004) J Mol Biol , vol.343 , pp. 1195-1206
    • Takamoto, K.1    Das, R.2    He, Q.3    Doniach, S.4    Brenowitz, M.5    Herschlag, D.6    Chance, M.R.7
  • 73
    • 16244384381 scopus 로고    scopus 로고
    • Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte
    • doi: 10.1062/1.1842059
    • Tan ZJ, Chen SJ. 2005. Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. J Chem Phys 122: 44903. doi: 10.1062/1.1842059.
    • (2005) J Chem Phys , vol.122 , pp. 44903
    • Tan, Z.J.1    Chen, S.J.2
  • 75
    • 47749120240 scopus 로고    scopus 로고
    • Salt dependence of nucleic acid hairpin stability
    • Tan ZJ, Chen SJ. 2008. Salt dependence of nucleic acid hairpin stability. Biophys J 95: 738-752.
    • (2008) Biophys J , vol.95 , pp. 738-752
    • Tan, Z.J.1    Chen, S.J.2
  • 76
    • 33846804221 scopus 로고    scopus 로고
    • Calculation of pKas in RNA: On the structural origins and functional roles of protonated nucleotides
    • Tang CL, Alexov E, Pyle AM, Honig B. 2007. Calculation of pKas in RNA: On the structural origins and functional roles of protonated nucleotides. J Mol Biol 366: 1475-1496.
    • (2007) J Mol Biol , vol.366 , pp. 1475-1496
    • Tang, C.L.1    Alexov, E.2    Pyle, A.M.3    Honig, B.4
  • 77
    • 33744469562 scopus 로고    scopus 로고
    • Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
    • Thore S, Leibundgut M, Ban N. 2006. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312: 1208-1211.
    • (2006) Science , vol.312 , pp. 1208-1211
    • Thore, S.1    Leibundgut, M.2    Ban, N.3
  • 78
    • 46049091176 scopus 로고    scopus 로고
    • Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch
    • Thore S, Frick C, Ban N. 2008. Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch. J Am Chem Soc 130: 8116-8117.
    • (2008) J Am Chem Soc , vol.130 , pp. 8116-8117
    • Thore, S.1    Frick, C.2    Ban, N.3
  • 79
    • 34447521717 scopus 로고    scopus 로고
    • Low specificity of metal ion binding in the metal ion core of a folded RNA
    • Travers KJ, Boyd N, Herschlag D. 2007. Low specificity of metal ion binding in the metal ion core of a folded RNA. RNA 13: 1205-1213.
    • (2007) RNA , vol.13 , pp. 1205-1213
    • Travers, K.J.1    Boyd, N.2    Herschlag, D.3
  • 80
  • 81
    • 1642586299 scopus 로고    scopus 로고
    • Control of gene expression by a natural metabolite-responsive ribozyme
    • Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
    • (2004) Nature , vol.428 , pp. 281-286
    • Winkler, W.C.1    Nahvi, A.2    Roth, A.3    Collins, J.A.4    Breaker, R.R.5
  • 82
    • 16244363320 scopus 로고    scopus 로고
    • Metal ions and RNA folding: A highly charged topic with a dynamic future
    • Woodson SA. 2005. Metal ions and RNA folding: A highly charged topic with a dynamic future. Curr Opin Chem Biol 9: 104-109.
    • (2005) Curr Opin Chem Biol , vol.9 , pp. 104-109
    • Woodson, S.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.