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Volumn 34, Issue , 2005, Pages 221-243

Ions and RNA folding

Author keywords

Electrostatics; Hydration; Magnesium; Poisson boltzmann theory; Potassium

Indexed keywords

ION;

EID: 20544448001     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.34.040204.144511     Document Type: Review
Times cited : (411)

References (96)
  • 1
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430:45-50
    • (2004) Nature , vol.430 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Kosek, A.B.3    Wang, J.4    Strobel, S.A.5
  • 2
    • 0018218514 scopus 로고
    • The hydrodynamic and spectroscopic properties of 16 S RNA from Escherichia coli ribosome in reconstitution buffer
    • Allen SH, Wong KP. 1978. The hydrodynamic and spectroscopic properties of 16 S RNA from Escherichia coli ribosome in reconstitution buffer. J. Biol. Chem. 253: 8759-66
    • (1978) J. Biol. Chem. , vol.253 , pp. 8759-8766
    • Allen, S.H.1    Wong, K.P.2
  • 3
    • 0023050126 scopus 로고
    • The role of magnesium and potassium ions in the molecular mechanism of ribosome assembly: Hydrodynamic, conformational, and thermal stability studies of 16S RNA from Escherichia coli ribosomes
    • Allen SH, Wong KP. 1986. The role of magnesium and potassium ions in the molecular mechanism of ribosome assembly: hydrodynamic, conformational, and thermal stability studies of 16S RNA from Escherichia coli ribosomes. Arch. Biochem. Biophys. 249:137-47
    • (1986) Arch. Biochem. Biophys. , vol.249 , pp. 137-147
    • Allen, S.H.1    Wong, K.P.2
  • 5
    • 0038539610 scopus 로고    scopus 로고
    • The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations
    • Auffinger P, Bielecki L, Westhof E. 2003. The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol. 10: 551-61
    • (2003) Chem. Biol. , vol.10 , pp. 551-561
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 7
    • 0346366808 scopus 로고    scopus 로고
    • 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations
    • 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol. 335:555-71
    • (2004) J. Mol. Biol. , vol.335 , pp. 555-571
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 8
    • 0034725528 scopus 로고    scopus 로고
    • Water and ion binding around RNA and DNA (C,G) oligomers
    • Auffinger P, Westhof E. 2000. Water and ion binding around RNA and DNA (C,G) oligomers. J. Mol. Biol. 300:1113-31
    • (2000) J. Mol. Biol. , vol.300 , pp. 1113-1131
    • Auffinger, P.1    Westhof, E.2
  • 9
    • 12844260994 scopus 로고    scopus 로고
    • Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
    • Bai Y, Das R, Millett IS, Herschlag D, Doniach S. 2004. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc. Natl. Acad. Sci. USA. 102:1035-40
    • (2004) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 1035-1040
    • Bai, Y.1    Das, R.2    Millett, I.S.3    Herschlag, D.4    Doniach, S.5
  • 11
    • 0036786231 scopus 로고    scopus 로고
    • Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly
    • Batey RT, Doudna JA. 2002. Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly. Biochemistry 41:11703-10
    • (2002) Biochemistry , vol.41 , pp. 11703-11710
    • Batey, R.T.1    Doudna, J.A.2
  • 12
    • 0031447208 scopus 로고    scopus 로고
    • DNA condensation by multivalent cations
    • Bloomfield VA. 1997. DNA condensation by multivalent cations. Biopolymers 44:269-82
    • (1997) Biopolymers , vol.44 , pp. 269-282
    • Bloomfield, V.A.1
  • 14
    • 0002452194 scopus 로고
    • NMR studies of cation-binding environments on nucleic acids
    • Braunlin WH. 1995. NMR studies of cation-binding environments on nucleic acids. Adv. Biophys. Chem. 5:89-139
    • (1995) Adv. Biophys. Chem. , vol.5 , pp. 89-139
    • Braunlin, W.H.1
  • 16
    • 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. 274:1020-31
    • (1997) J. Mol. Biol. , vol.274 , pp. 1020-1031
    • Bukhman, Y.V.1    Draper, D.E.2
  • 17
    • 0029820625 scopus 로고    scopus 로고
    • Crystal structure of a group I ribozyme domain: Principles of RNA packing
    • Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, et al. 1996. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273:1678-85
    • (1996) Science , vol.273 , pp. 1678-1685
    • Cate, J.H.1    Gooding, A.R.2    Podell, E.3    Zhou, K.4    Golden, B.L.5
  • 18
    • 0030929889 scopus 로고    scopus 로고
    • A magnesium ion core at the heart of a ribozyme domain
    • Gate JH, Hanna RL, Doudna JA. 1997. A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol. 4:553-58
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 553-558
    • Gate, J.H.1    Hanna, R.L.2    Doudna, J.A.3
  • 19
    • 2942547665 scopus 로고    scopus 로고
    • Simulation and modeling of nucleic acid structure, dynamics and interactions
    • Cheatham TE 3rd. 2004. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 14:360-67
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 360-367
    • Cheatham III, T.E.1
  • 20
    • 0031249752 scopus 로고    scopus 로고
    • Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poisson-Boltzmann equation: Application to DNA binding reactions
    • Chen SW, Honig B. 1997. Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poisson-Boltzmann equation: application to DNA binding reactions. J. Phys. Chem. B 101:9113-18
    • (1997) J. Phys. Chem. B , vol.101 , pp. 9113-9118
    • Chen, S.W.1    Honig, B.2
  • 21
    • 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. 6:1055-61
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 1055-1061
    • Chin, K.1    Sharp, K.A.2    Honig, B.3    Pyle, A.M.4
  • 22
    • 0015497450 scopus 로고
    • Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams
    • Cole PE, Yang SK, Crothers DM. 1972. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry 11:4358-68
    • (1972) Biochemistry , vol.11 , pp. 4358-4368
    • Cole, P.E.1    Yang, S.K.2    Crothers, D.M.3
  • 23
    • 0033516616 scopus 로고    scopus 로고
    • Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme
    • Colmenarejo G, Tinoco I Jr. 1999. Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme. J. Mol. Biol. 290:119-35
    • (1999) J. Mol. Biol. , vol.290 , pp. 119-135
    • Colmenarejo, G.1    Tinoco Jr., I.2
  • 25
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
    • Correll CC, Freeborn B, Moore PB, Steitz TA. 1997. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91:705-12
    • (1997) Cell , vol.91 , pp. 705-712
    • Correll, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 27
  • 29
    • 84985666936 scopus 로고
    • Cation effects on the denaturation of DNA
    • Dove WF, Davidson N. 1962. Cation effects on the denaturation of DNA. J. Mol. Biol. 5:467-78
    • (1962) J. Mol. Biol. , vol.5 , pp. 467-478
    • Dove, W.F.1    Davidson, N.2
  • 31
    • 1242274330 scopus 로고    scopus 로고
    • A guide to ions and RNA structure
    • Draper DE. 2004. A guide to ions and RNA structure. RNA 10:335-43
    • (2004) RNA , vol.10 , pp. 335-343
    • Draper, D.E.1
  • 32
    • 0017869404 scopus 로고
    • Water and proteins. I. The significance and structure of water; its interaction with electrolytes and non-electrolytes
    • Edsall JT, McKenzie HA. 1978. Water and proteins. I. The significance and structure of water; its interaction with electrolytes and non-electrolytes. Adv. Biophys. 10:137-207
    • (1978) Adv. Biophys. , vol.10 , pp. 137-207
    • Edsall, J.T.1    McKenzie, H.A.2
  • 33
    • 0021070747 scopus 로고
    • Ionic selectivity revisited: The role of kinetic and equilibrium processes in ion permeation through channels
    • Eisenman G, Horn R. 1983. Ionic selectivity revisited: the role of kinetic and equilibrium processes in ion permeation through channels. J. Membr. Biol. 76:197-225
    • (1983) J. Membr. Biol. , vol.76 , pp. 197-225
    • Eisenman, G.1    Horn, R.2
  • 34
    • 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. 31:2671-82
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2671-2682
    • Ennifar, E.1    Walter, P.2    Dumas, P.3
  • 35
    • 0035184520 scopus 로고    scopus 로고
    • Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site
    • Ennifar E, Walter P, Ehresmann B, Ehresmann C, Dumas P. 2001. Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat. Struct. Biol. 8:1064-68
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 1064-1068
    • Ennifar, E.1    Walter, P.2    Ehresmann, B.3    Ehresmann, C.4    Dumas, P.5
  • 36
    • 0033571104 scopus 로고    scopus 로고
    • The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
    • Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, et al. 1999. The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges. Struct. Fold Des. 7:1439-49
    • (1999) Struct. Fold Des. , vol.7 , pp. 1439-1449
    • Ennifar, E.1    Yusupov, M.2    Walter, P.3    Marquet, R.4    Ehresmann, B.5
  • 37
    • 0034641612 scopus 로고    scopus 로고
    • Phe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering
    • Phe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 39:11107-13
    • (2000) Biochemistry , vol.39 , pp. 11107-11113
    • Fang, X.1    Littrell, K.2    Yang, X.J.3    Henderson, S.J.4    Siefert, S.5
  • 39
    • 0036601149 scopus 로고    scopus 로고
    • The role of metal ions in RNA catalysis
    • Fedor MJ. 2002. The role of metal ions in RNA catalysis. Curr. Opin. Struct. Biol. 12:289-95
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 289-295
    • Fedor, M.J.1
  • 40
    • 0033231004 scopus 로고    scopus 로고
    • Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy
    • Feig AL, Panek M, Horrocks WD Jr, Uhlenbeck OC. 1999. Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy. Chem. Biol. 6:801-10
    • (1999) Chem. Biol. , vol.6 , pp. 801-810
    • Feig, A.L.1    Panek, M.2    Horrocks Jr., W.D.3    Uhlenbeck, O.C.4
  • 41
    • 0032851951 scopus 로고    scopus 로고
    • Sodium and chlorine ions as part of the DNA solvation shell
    • Feig M, Pettitt BM. 1999. Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J. 77:1769-81
    • (1999) Biophys. J. , vol.77 , pp. 1769-1781
    • Feig, M.1    Pettitt, B.M.2
  • 42
    • 0038499698 scopus 로고    scopus 로고
    • Electrostatic interactions in a peptide-RNA complex
    • García-García C, Draper DE. 2003. Electrostatic interactions in a peptide-RNA complex. J. Mol. Biol. 331:75-88
    • (2003) J. Mol. Biol. , vol.331 , pp. 75-88
    • García-García, C.1    Draper, D.E.2
  • 43
    • 0345299164 scopus 로고    scopus 로고
    • Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudo-knot
    • Gonzalez RL Jr, Tinoco I Jr. 1999. Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudo-knot. J. Mol. Biol. 289:1267-82
    • (1999) J. Mol. Biol. , vol.289 , pp. 1267-1282
    • Gonzalez Jr., R.L.1    Tinoco Jr., I.2
  • 44
    • 0035969972 scopus 로고    scopus 로고
    • Probing of metal-binding domains of RNA hairpin loops by laser-induced lanthanide(III) luminescence
    • Greenbaum NL, Mundoma C, Peterman DR. 2001. Probing of metal-binding domains of RNA hairpin loops by laser-induced lanthanide(III) luminescence. Biochemistry 40:1124-34
    • (2001) Biochemistry , vol.40 , pp. 1124-1134
    • Greenbaum, N.L.1    Mundoma, C.2    Peterman, D.R.3
  • 45
    • 0021930512 scopus 로고
    • Interactions of some naturally occurring cations with phenylalanine and initiator tRNA from yeast as reflected by their thermal stability
    • Heerschap A, Walters JALI, Hilbers CW. 1985. Interactions of some naturally occurring cations with phenylalanine and initiator tRNA from yeast as reflected by their thermal stability. Biophys. Chem. 22:205-17
    • (1985) Biophys. Chem. , vol.22 , pp. 205-217
    • Heerschap, A.1    Jali, W.2    Hilbers, C.W.3
  • 46
    • 0035830964 scopus 로고    scopus 로고
    • Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations
    • Heilman-Miller SL, Thirumalai D, Woodson SA. 2001. Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J. Mol. Biol. 306:1157-66
    • (2001) J. Mol. Biol. , vol.306 , pp. 1157-1166
    • Heilman-Miller, S.L.1    Thirumalai, D.2    Woodson, S.A.3
  • 49
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. 1995. Classical electrostatics in biology and chemistry. Science 268:1144-49
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 50
    • 0036215617 scopus 로고    scopus 로고
    • Water counting: Quantitating the hydration level of paramagnetic metal ions bound to nucleotides and nucleic acids
    • Hoogstraten CG, Britt RD. 2002. Water counting: quantitating the hydration level of paramagnetic metal ions bound to nucleotides and nucleic acids. RNA 8:252-60
    • (2002) RNA , vol.8 , pp. 252-260
    • Hoogstraten, C.G.1    Britt, R.D.2
  • 51
    • 0037028557 scopus 로고    scopus 로고
    • Structural analysis of metal ion ligation to nucleotides and nucleic acids using pulsed EPR spectroscopy
    • Hoogstraten CG, Grant CV, Horton TE, DeRose VJ, Britt RD. 2002. Structural analysis of metal ion ligation to nucleotides and nucleic acids using pulsed EPR spectroscopy. J. Am. Chem. Soc. 124:834-42
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 834-842
    • Hoogstraten, C.G.1    Grant, C.V.2    Horton, T.E.3    Derose, V.J.4    Britt, R.D.5
  • 52
    • 0017786103 scopus 로고
    • Laser-induced lanthanide ion luminescence lifetime measurements by direct excitation of metal ion levels. A new class of structural probe for calcium-binding proteins and nucleic acids
    • Horrocks WD Jr, Schmidt GF, Sudnick DR, Kittrell C, Bernheim RA. 1977. Laser-induced lanthanide ion luminescence lifetime measurements by direct excitation of metal ion levels. A new class of structural probe for calcium-binding proteins and nucleic acids. J. Am. Chem. Soc. 99:2378-80
    • (1977) J. Am. Chem. Soc. , vol.99 , pp. 2378-2380
    • Horrocks Jr., W.D.1    Schmidt, G.F.2    Sudnick, D.R.3    Kittrell, C.4    Bernheim, R.A.5
  • 53
    • 0032559057 scopus 로고    scopus 로고
    • Electron paramagnetic resonance spectroscopic measurement of Mn2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity
    • Horton TE, Clardy DR, DeRose VJ. 1998. Electron paramagnetic resonance spectroscopic measurement of Mn2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity. Biochemistry 37:18094-101
    • (1998) Biochemistry , vol.37 , pp. 18094-18101
    • Horton, T.E.1    Clardy, D.R.2    DeRose, V.J.3
  • 55
    • 0017361887 scopus 로고
    • A crystallographic study of metal-binding to yeast phenylalanine transfer RNA
    • Jack A, Ladner JE, Rhodes D, Brown RS, Klug A. 1977. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J. Mol. Biol. 111:315-28
    • (1977) J. Mol. Biol. , vol.111 , pp. 315-328
    • Jack, A.1    Ladner, J.E.2    Rhodes, D.3    Brown, R.S.4    Klug, A.5
  • 56
    • 0034636993 scopus 로고    scopus 로고
    • The crystal structure of yeast phenylalanine tRNA at 2.0 ÅA resolution: Cleavage by Mg(2+) in 15-year old crystals
    • Jovine L, Djordjevic S, Rhodes D. 2000. The crystal structure of yeast phenylalanine tRNA at 2.0 ÅA resolution: cleavage by Mg(2+) in 15-year old crystals. J. Mol. Biol. 301:401-14
    • (2000) J. Mol. Biol. , vol.301 , pp. 401-414
    • Jovine, L.1    Djordjevic, S.2    Rhodes, D.3
  • 57
    • 0035085466 scopus 로고    scopus 로고
    • Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions
    • Juneau K, Podell E, Harrington DJ, Cech TR. 2001. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure 9:221-31
    • (2001) Structure , vol.9 , pp. 221-231
    • Juneau, K.1    Podell, E.2    Harrington, D.J.3    Cech, T.R.4
  • 58
    • 0031570344 scopus 로고    scopus 로고
    • Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine
    • Kieft JS, Tinoco I. 1997. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine. Structure 5:713-21
    • (1997) Structure , vol.5 , pp. 713-721
    • Kieft, J.S.1    Tinoco, I.2
  • 59
    • 4344569647 scopus 로고    scopus 로고
    • The contribution of metal ions to the structural stability of the large ribosomal subunit
    • Klein DJ, Moore PB, Steitz TA. 2004. The contribution of metal ions to the structural stability of the large ribosomal subunit. RNA 10:1366-79
    • (2004) RNA , vol.10 , pp. 1366-1379
    • Klein, D.J.1    Moore, P.B.2    Steitz, T.A.3
  • 60
    • 0019888458 scopus 로고
    • The molecular electrostatic potential and steric accessibility of A-DNA
    • Lavery R, Pullman B. 1981. The molecular electrostatic potential and steric accessibility of A-DNA. Nucleic Acids Res. 9:4677-88
    • (1981) Nucleic Acids Res. , vol.9 , pp. 4677-4688
    • Lavery, R.1    Pullman, B.2
  • 61
    • 0017657694 scopus 로고
    • Electrostatic effects in divalent ion binding to tRNA
    • Leroy JL, Guéron M. 1977. Electrostatic effects in divalent ion binding to tRNA. Biopolymers 16:2429-46
    • (1977) Biopolymers , vol.16 , pp. 2429-2446
    • Leroy, J.L.1    Guéron, M.2
  • 62
    • 0028102703 scopus 로고
    • Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA
    • Lu M, Draper DE. 1994. Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA. J. Mol. Biol. 244:572-85
    • (1994) J. Mol. Biol. , vol.244 , pp. 572-585
    • Lu, M.1    Draper, D.E.2
  • 63
    • 0037118418 scopus 로고    scopus 로고
    • The arrangement of first- And second-sphere water molecules in divalent magnesium complexes: Results from molecular orbital and density functional theory and from structural crystallography
    • Markham GD, Glusker JP, Bock CW. 2002. The arrangement of first- and second-sphere water molecules in divalent magnesium complexes: results from molecular orbital and density functional theory and from structural crystallography. J. Phys. Chem. B 106:5118-34
    • (2002) J. Phys. Chem. B , vol.106 , pp. 5118-5134
    • Markham, G.D.1    Glusker, J.P.2    Bock, C.W.3
  • 64
    • 0032419499 scopus 로고    scopus 로고
    • On the role of magnesium ions in RNA stability
    • Misra VK, Draper DE. 1998. On the role of magnesium ions in RNA stability. Biopolymers 48:113-35
    • (1998) Biopolymers , vol.48 , pp. 113-135
    • Misra, V.K.1    Draper, D.E.2
  • 65
    • 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. 294:1135-47
    • (1999) J. Mol. Biol. , vol.294 , pp. 1135-1147
    • Misra, V.K.1    Draper, D.E.2
  • 66
    • 0034625314 scopus 로고    scopus 로고
    • Mg(2+) binding to tRNA revisited: The nonlinear Poisson-Boltzmann model
    • Misra VK, Draper DE. 2000. Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model. J. Mol. Biol. 299:813-25
    • (2000) J. Mol. Biol. , vol.299 , pp. 813-825
    • Misra, V.K.1    Draper, D.E.2
  • 68
    • 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. 317:507-21
    • (2002) J. Mol. Biol. , vol.317 , pp. 507-521
    • Misra, V.K.1    Draper, D.E.2
  • 69
    • 0038713248 scopus 로고    scopus 로고
    • A thermodynamic framework for the magnesium-dependent folding of RNA
    • Misra VK, Shiman R, Draper DE. 2003. A thermodynamic framework for the magnesium-dependent folding of RNA. Biopolymers 69:118-36
    • (2003) Biopolymers , vol.69 , pp. 118-136
    • Misra, V.K.1    Shiman, R.2    Draper, D.E.3
  • 71
    • 0034727663 scopus 로고    scopus 로고
    • Is counterion delocalization responsible for collapse in RNA folding?
    • Murthy VL, Rose GD. 2000. Is counterion delocalization responsible for collapse in RNA folding? Biochemistry 39:14365-70
    • (2000) Biochemistry , vol.39 , pp. 14365-14370
    • Murthy, V.L.1    Rose, G.D.2
  • 73
    • 0037188003 scopus 로고    scopus 로고
    • Water-mediated magnesium-guanine interactions
    • Petrov AS, Pack GR, Lamm G. 2002. Water-mediated magnesium-guanine interactions. J. Phys. Chem. 106:3294-300
    • (2002) J. Phys. Chem. , vol.106 , pp. 3294-3300
    • Petrov, A.S.1    Pack, G.R.2    Lamm, G.3
  • 74
    • 2542443314 scopus 로고    scopus 로고
    • Calculations of magnesium-nucleic acid site binding in solution
    • Petrov AS, Pack GR, Lamm G. 2004. Calculations of magnesium-nucleic acid site binding in solution. J. Phys. Chem. 108: 6072-81
    • (2004) J. Phys. Chem. , vol.108 , pp. 6072-6081
    • Petrov, A.S.1    Pack, G.R.2    Lamm, G.3
  • 75
    • 0008875663 scopus 로고
    • Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA
    • Quigley GJ, Teeter MM, Rich A. 1978. Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc. Natl. Acad. Sci. USA 75:64-68
    • (1978) Proc. Natl. Acad. Sci. USA , vol.75 , pp. 64-68
    • Quigley, G.J.1    Teeter, M.M.2    Rich, A.3
  • 76
    • 0037764044 scopus 로고    scopus 로고
    • Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E
    • Reblova K, Spackova N, Stefl R, Csaszar K, Koca J, et al. 2003. Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys. J. 84:3564-82
    • (2003) Biophys. J. , vol.84 , pp. 3564-3582
    • Reblova, K.1    Spackova, N.2    Stefl, R.3    Csaszar, K.4    Koca, J.5
  • 77
    • 1242348493 scopus 로고
    • Physical chemical analysis of biopolymer self-assembly interactions
    • ed. ET Lippincott. Washington, DC: Am. Chem. Soc.
    • Record MT Jr, Richey B. 1988. Physical chemical analysis of biopolymer self-assembly interactions. In ACS Sourcebook for Physical Chemistry Instructors, ed. ET Lippincott, pp. 145-59. Washington, DC: Am. Chem. Soc.
    • (1988) ACS Sourcebook for Physical Chemistry Instructors , pp. 145-159
    • Record Jr., M.T.1    Richey, B.2
  • 78
    • 0031776135 scopus 로고    scopus 로고
    • Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts
    • Record MT Jr, Zhang W, Anderson CF. 1998. Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv. Protein Chem. 51:281-353
    • (1998) Adv. Protein Chem. , vol.51 , pp. 281-353
    • Record Jr., M.T.1    Zhang, W.2    Anderson, C.F.3
  • 80
    • 0034655642 scopus 로고    scopus 로고
    • Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes
    • Robinson H, Gao YG, Sanishvili R, Joachimiak A, Wang AH. 2000. Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes. Nucleic Acids Res. 28:1760-66
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1760-1766
    • Robinson, H.1    Gao, Y.G.2    Sanishvili, R.3    Joachimiak, A.4    Wang, A.H.5
  • 81
    • 0016732394 scopus 로고
    • tRNA conformation and magnesium binding. A study of a yeast phenylalanine-specific tRNA by a fluorescent indicator and differential melting curves
    • Römer R, Hach R. 1975. tRNA conformation and magnesium binding. A study of a yeast phenylalanine-specific tRNA by a fluorescent indicator and differential melting curves. Eur. J. Biochem. 55:271-84
    • (1975) Eur. J. Biochem. , vol.55 , pp. 271-284
    • Römer, R.1    Hach, R.2
  • 82
    • 0037468432 scopus 로고    scopus 로고
    • 2+) in the presence and absence of nucleobase. The role of nonelectrostatic effects
    • 2+) in the presence and absence of nucleobase. The role of nonelectrostatic effects. J. Phys. Chem. 107:1913-23
    • (2003) J. Phys. Chem. , vol.107 , pp. 1913-1923
    • Rulisek, L.1    Sponer, J.2
  • 83
    • 0034100560 scopus 로고    scopus 로고
    • Small angle X-ray scattering reveals a compact intermediate in RNA folding
    • Russell R, Millett IS, Doniach S, Herschlag D. 2000. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat. Struct. Biol. 7:367-70
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 367-370
    • Russell, R.1    Millett, I.S.2    Doniach, S.3    Herschlag, D.4
  • 86
    • 0033862354 scopus 로고    scopus 로고
    • The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited
    • Shi H, Moore PB. 2000. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA 6:1091-105
    • (2000) RNA , vol.6 , pp. 1091-1105
    • Shi, H.1    Moore, P.B.2
  • 87
    • 0034622981 scopus 로고    scopus 로고
    • Stabilization of RNA tertiary structure by monovalent cations
    • Shiman R, Draper DE. 2000. Stabilization of RNA tertiary structure by monovalent cations. J. Mol. Biol. 302:79-91
    • (2000) J. Mol. Biol. , vol.302 , pp. 79-91
    • Shiman, R.1    Draper, D.E.2
  • 88
    • 0033529336 scopus 로고    scopus 로고
    • Energetics and cooperativity of tertiary hydrogen bonds in RNA structure
    • Silverman SK, Cech TR. 1999. Energetics and cooperativity of tertiary hydrogen bonds in RNA structure. Biochemistry 38:8691-702
    • (1999) Biochemistry , vol.38 , pp. 8691-8702
    • Silverman, S.K.1    Cech, T.R.2
  • 89
    • 0017295709 scopus 로고
    • Conformational changes of transfer RNA. The role of magnesium(n)
    • Stein A, Crothers DM. 1976. Conformational changes of transfer RNA. The role of magnesium(n). Biochemistry 15:160-67
    • (1976) Biochemistry , vol.15 , pp. 160-167
    • Stein, A.1    Crothers, D.M.2
  • 90
    • 0016044321 scopus 로고
    • Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0 Angstroms resolution
    • Suddath FL, Quigley GJ, McPherson A, Sneden D, Kim JJ, et al. 1974. Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0 Angstroms resolution. Nature 248:20-24
    • (1974) Nature , vol.248 , pp. 20-24
    • Suddath, F.L.1    Quigley, G.J.2    McPherson, A.3    Sneden, D.4    Kim, J.J.5
  • 91
    • 0036894697 scopus 로고    scopus 로고
    • Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme
    • TakamotoK, He Q, Morris S, Chance MR, Brenowitz M. 2002. Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme. Nat. Struct. Biol. 9:928-33
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 928-933
    • Takamoto, K.1    He, Q.2    Morris, S.3    Chance, M.R.4    Brenowitz, M.5
  • 92
    • 0035283086 scopus 로고    scopus 로고
    • Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments
    • Tereshko V, Wilds CJ, Minasov G, Prakash TP, Maier MA, et al. 2001. Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. Nucleic Acids Res. 29:1208-15
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1208-1215
    • Tereshko, V.1    Wilds, C.J.2    Minasov, G.3    Prakash, T.P.4    Maier, M.A.5
  • 93
    • 0035892161 scopus 로고    scopus 로고
    • Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics
    • Tsui V, Case DA. 2001. Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics. J. Phys. Chem. 2001:11314-25
    • (2001) J. Phys. Chem. , vol.2001 , pp. 11314-11325
    • Tsui, V.1    Case, D.A.2
  • 95
    • 0035156627 scopus 로고    scopus 로고
    • A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex
    • Webb AE, Weeks KM. 2001. A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex. Nat. Struct. Biol. 8:135-40
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 135-140
    • Webb, A.E.1    Weeks, K.M.2
  • 96
    • 0032578472 scopus 로고    scopus 로고
    • RNA folding causes secondary structure rearrangement
    • Wu M, Tinoco I Jr. 1998. RNA folding causes secondary structure rearrangement. Proc. Natl. Acad. Sci. USA 95:11555-60
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 11555-11560
    • Wu, M.1    Tinoco Jr., I.2


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