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Volumn 341, Issue 1, 2004, Pages 27-36

Folding of the Tetrahymena ribozyme by polyamines: Importance of counterion valence and size

Author keywords

BD, Brownian dynamics; counterion condensation; group I ribozyme; polyamines; RNA folding

Indexed keywords

MAGNESIUM; PHOSPHATE; POLYAMINE; POLYELECTROLYTE; RIBOZYME;

EID: 4143072545     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.06.008     Document Type: Article
Times cited : (54)

References (47)
  • 1
    • 0032419499 scopus 로고    scopus 로고
    • On the role of magnesium ions in RNA stability
    • Misra V.K., Draper D.E. On the role of magnesium ions in RNA stability. Biopolymers. 48:1998;113-135
    • (1998) Biopolymers , vol.48 , pp. 113-135
    • Misra, V.K.1    Draper, D.E.2
  • 3
    • 0032727991 scopus 로고    scopus 로고
    • Themes in RNA-protein recognition
    • Draper D.E. Themes in RNA-protein recognition. J. Mol. Biol. 293:1999;255-270
    • (1999) J. Mol. Biol. , vol.293 , pp. 255-270
    • Draper, D.E.1
  • 5
    • 0034685624 scopus 로고    scopus 로고
    • Polyamines: Mysterious modulators of cellular functions
    • Igarashi K., Kashiwagi K. Polyamines: mysterious modulators of cellular functions. Biochem. Biophys. Res. Commun. 271:2000;559-564
    • (2000) Biochem. Biophys. Res. Commun. , vol.271 , pp. 559-564
    • Igarashi, K.1    Kashiwagi, K.2
  • 7
    • 0034678904 scopus 로고    scopus 로고
    • Conservation of polyamine regulation by translational frameshifting from yeast to mammals
    • Ivanov I.P., Matsufuji S., Murakami Y., Gesteland R.F., Atkins J.F. Conservation of polyamine regulation by translational frameshifting from yeast to mammals. EMBO J. 19:2000;1907-1917
    • (2000) EMBO J. , vol.19 , pp. 1907-1917
    • Ivanov, I.P.1    Matsufuji, S.2    Murakami, Y.3    Gesteland, R.F.4    Atkins, J.F.5
  • 8
  • 9
    • 0019027984 scopus 로고
    • Polyelectrolyte effects in DNA condensation by polyamines
    • Bloomfield V.A., Wilson R.W., Rau D.C. Polyelectrolyte effects in DNA condensation by polyamines. Biophys. Chem. 11:1980;339-343
    • (1980) Biophys. Chem. , vol.11 , pp. 339-343
    • Bloomfield, V.A.1    Wilson, R.W.2    Rau, D.C.3
  • 10
    • 0025823653 scopus 로고
    • Polyamines favor DNA triplex formation at neutral pH
    • Hampel K.J., Crosson P., Lee J.S. Polyamines favor DNA triplex formation at neutral pH. Biochemistry. 30:1991;4455-4459
    • (1991) Biochemistry , vol.30 , pp. 4455-4459
    • Hampel, K.J.1    Crosson, P.2    Lee, J.S.3
  • 11
    • 0027743418 scopus 로고
    • Selectivity of polyamines in triplex DNA stabilization
    • Thomas T., Thomas T.J. Selectivity of polyamines in triplex DNA stabilization. Biochemistry. 32:1993;14068-14074
    • (1993) Biochemistry , vol.32 , pp. 14068-14074
    • Thomas, T.1    Thomas, T.J.2
  • 12
    • 0033578337 scopus 로고    scopus 로고
    • Selectivity of polyamines on the stability of RNA-DNA hybrids containing phosphodiester and phosphorothioate oligodeoxyribonucleotides
    • Antony T., Thomas T., Shirahata A., Thomas T.J. Selectivity of polyamines on the stability of RNA-DNA hybrids containing phosphodiester and phosphorothioate oligodeoxyribonucleotides. Biochemistry. 38:1999;10775-10784
    • (1999) Biochemistry , vol.38 , pp. 10775-10784
    • Antony, T.1    Thomas, T.2    Shirahata, A.3    Thomas, T.J.4
  • 13
    • 0024546799 scopus 로고
    • Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC)
    • Jain S., Zon G., Sundaralingam M. Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC). Biochemistry. 28:1989;2360-2364
    • (1989) Biochemistry , vol.28 , pp. 2360-2364
    • Jain, S.1    Zon, G.2    Sundaralingam, M.3
  • 14
    • 0008875663 scopus 로고
    • Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA
    • Quigley G.J., Teeter M.M., Rich A. Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc. Natl Acad. Sci. USA. 75:1978;64-68
    • (1978) Proc. Natl Acad. Sci. USA , vol.75 , pp. 64-68
    • Quigley, G.J.1    Teeter, M.M.2    Rich, A.3
  • 15
    • 0019942441 scopus 로고
    • Equilibrium dialysis studies of polyamine binding to DNA
    • Braunlin W.H., Strick T.J., Record M.T. Jr. Equilibrium dialysis studies of polyamine binding to DNA. Biopolymers. 21:1982;1301-1314
    • (1982) Biopolymers , vol.21 , pp. 1301-1314
    • Braunlin, W.H.1    Strick, T.J.2    Record Jr., M.T.3
  • 16
    • 0022429605 scopus 로고
    • Nuclear magnetic resonance studies of polyamine binding to a defined DNA sequence
    • Wemmer D.E., Srivenugopal K.S., Reid B.R., Morris D.R. Nuclear magnetic resonance studies of polyamine binding to a defined DNA sequence. J. Mol. Biol. 185:1985;457-459
    • (1985) J. Mol. Biol. , vol.185 , pp. 457-459
    • Wemmer, D.E.1    Srivenugopal, K.S.2    Reid, B.R.3    Morris, D.R.4
  • 17
    • 0034284109 scopus 로고    scopus 로고
    • Structural basis of polyamine-DNA recognition: Spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy
    • Deng H., Bloomfield V.A., Benevides J.M., Thomas G.J. Jr. Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Nucl. Acids Res. 28:2000;3379-3385
    • (2000) Nucl. Acids Res. , vol.28 , pp. 3379-3385
    • Deng, H.1    Bloomfield, V.A.2    Benevides, J.M.3    Thomas Jr., G.J.4
  • 18
    • 0026253815 scopus 로고
    • Condensation of DNA by multivalent cations: Considerations on mechanism
    • Bloomfield V.A. Condensation of DNA by multivalent cations: considerations on mechanism. Biopolymers. 31:1991;1471-1481
    • (1991) Biopolymers , vol.31 , pp. 1471-1481
    • Bloomfield, V.A.1
  • 19
    • 0035830964 scopus 로고    scopus 로고
    • Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations
    • Heilman-Miller S.L., Thirumalai D., Woodson S.A. Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J. Mol. Biol. 306:2001;1157-1166
    • (2001) J. Mol. Biol. , vol.306 , pp. 1157-1166
    • Heilman-Miller, S.L.1    Thirumalai, D.2    Woodson, S.A.3
  • 20
    • 0033065083 scopus 로고    scopus 로고
    • Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics
    • Pan J., Thirumalai D., Woodson S.A. Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc. Natl Acad. Sci. USA. 96:1999;6149-6154
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 6149-6154
    • Pan, J.1    Thirumalai, D.2    Woodson, S.A.3
  • 23
    • 0034641612 scopus 로고    scopus 로고
    • 2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering
    • 2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry. 39:2000;11107-11113
    • (2000) Biochemistry , vol.39 , pp. 11107-11113
    • Fang, X.1    Littrell, K.2    Yang, X.J.3    Henderson, S.J.4    Siefert, S.5    Thiyagarajan, P.6
  • 24
    • 0034100560 scopus 로고    scopus 로고
    • Small angle X-ray scattering reveals a compact intermediate in RNA folding
    • Russell R., Millett I.S., Doniach S., Herschlag D. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nature Struct. Biol. 7:2000;367-370
    • (2000) Nature Struct. Biol. , vol.7 , pp. 367-370
    • Russell, R.1    Millett, I.S.2    Doniach, S.3    Herschlag, D.4
  • 27
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning G.S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quart. Rev. Biophys. 11:1978;179-246
    • (1978) Quart. Rev. Biophys. , vol.11 , pp. 179-246
    • Manning, G.S.1
  • 28
    • 0031447208 scopus 로고    scopus 로고
    • DNA condensation by multivalent cations
    • Bloomfield V.A. DNA condensation by multivalent cations. Biopolymers. 44:1997;269-282
    • (1997) Biopolymers , vol.44 , pp. 269-282
    • Bloomfield, V.A.1
  • 29
    • 0012848624 scopus 로고    scopus 로고
    • Influence of ligand spatial organization on competitive electrostatic binding to DNA
    • Rouzina I., Bloomfield V.A. Influence of ligand spatial organization on competitive electrostatic binding to DNA. J. Phys. Chem. 100:1996;4305-4313
    • (1996) J. Phys. Chem. , vol.100 , pp. 4305-4313
    • Rouzina, I.1    Bloomfield, V.A.2
  • 30
    • 0000959868 scopus 로고    scopus 로고
    • Reentrant condensation of DNA induced by multivalent counterions
    • Nguyen T.T., Rouzina I., Shklovskii B.I. Reentrant condensation of DNA induced by multivalent counterions. J. Chem. Phys. 112:2000;2562-2568
    • (2000) J. Chem. Phys. , vol.112 , pp. 2562-2568
    • Nguyen, T.T.1    Rouzina, I.2    Shklovskii, B.I.3
  • 32
    • 0036295964 scopus 로고    scopus 로고
    • The linkage between magnesium binding and RNA folding
    • Misra V.K., Draper D.E. The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317:2002;507-521
    • (2002) J. Mol. Biol. , vol.317 , pp. 507-521
    • Misra, V.K.1    Draper, D.E.2
  • 33
    • 0033579408 scopus 로고    scopus 로고
    • The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzmann theory
    • Misra V.K., Draper D.E. The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzmann theory. J. Mol. Biol. 294:1999;1135-1147
    • (1999) J. Mol. Biol. , vol.294 , pp. 1135-1147
    • Misra, V.K.1    Draper, D.E.2
  • 34
    • 0347653719 scopus 로고    scopus 로고
    • Bending rigidity of stiff polyelectrolyte chains: A single chain and bundle of multichains
    • Ha B.Y., Thirumalai D. Bending rigidity of stiff polyelectrolyte chains: a single chain and bundle of multichains. Macromolecules. 36:2003;9658-9666
    • (2003) Macromolecules , vol.36 , pp. 9658-9666
    • Ha, B.Y.1    Thirumalai, D.2
  • 35
    • 0029816432 scopus 로고    scopus 로고
    • Binding of ionic ligands to polyelectrolytes
    • Stigter D., Dill K.A. Binding of ionic ligands to polyelectrolytes. Biophys. J. 71:1996;2064-2074
    • (1996) Biophys. J. , vol.71 , pp. 2064-2074
    • Stigter, D.1    Dill, K.A.2
  • 36
    • 0014245160 scopus 로고
    • Topography of nucleic acid helices in solutions. 3. Interactions of spermine and spermidine derivatives with polyadenylic-polyuridylic and polyinosinic-polycytidylic acid helices
    • Glasser R., Gabbay E.J. Topography of nucleic acid helices in solutions. 3. Interactions of spermine and spermidine derivatives with polyadenylic- polyuridylic and polyinosinic-polycytidylic acid helices. Biopolymers. 6:1968;243-254
    • (1968) Biopolymers , vol.6 , pp. 243-254
    • Glasser, R.1    Gabbay, E.J.2
  • 38
    • 0025147762 scopus 로고
    • Condensation of DNA by trivalent cations. 2. Effects of cation structure
    • Plum G.E., Arscott P.G., Bloomfield V.A. Condensation of DNA by trivalent cations. 2. Effects of cation structure. Biopolymers. 30:1990;631-643
    • (1990) Biopolymers , vol.30 , pp. 631-643
    • Plum, G.E.1    Arscott, P.G.2    Bloomfield, V.A.3
  • 40
    • 0035856537 scopus 로고    scopus 로고
    • DNA condensation by polyamines: A laser light scattering study of structural effects
    • Vijayanathan V., Thomas T., Shirahata A., Thomas T.J. DNA condensation by polyamines: a laser light scattering study of structural effects. Biochemistry. 40:2001;13644-13651
    • (2001) Biochemistry , vol.40 , pp. 13644-13651
    • Vijayanathan, V.1    Thomas, T.2    Shirahata, A.3    Thomas, T.J.4
  • 41
    • 0034635353 scopus 로고    scopus 로고
    • Fast folding of a ribozyme by stabilizing core interactions: Evidence for multiple folding pathways in RNA
    • Pan J., Deras M.L., Woodson S.A. Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA. J. Mol. Biol. 296:2000;133-144
    • (2000) J. Mol. Biol. , vol.296 , pp. 133-144
    • Pan, J.1    Deras, M.L.2    Woodson, S.A.3
  • 42
    • 0027940350 scopus 로고
    • Fingerprinting the folding of a group I precursor RNA
    • Emerick V.L., Woodson S.A. Fingerprinting the folding of a group I precursor RNA. Proc. Natl Acad. Sci. USA. 91:1994;9675-9679
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 9675-9679
    • Emerick, V.L.1    Woodson, S.A.2
  • 43
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
    • Record M.T. Jr, Anderson C.F., Lohman T.M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Quart. Rev. Biophys. 11:1978;103-178
    • (1978) Quart. Rev. Biophys. , vol.11 , pp. 103-178
    • Record Jr., M.T.1    Anderson, C.F.2    Lohman, T.M.3
  • 44
    • 0025786032 scopus 로고
    • Relative affinities of divalent polyamines and of their N-methylated analogues for helical DNA determined by 23Na NMR
    • Padmanabhan S., Brushaber V.M., Anderson C.F., Record M.T. Jr. Relative affinities of divalent polyamines and of their N-methylated analogues for helical DNA determined by 23Na NMR. Biochemistry. 30:1991;7550-7559
    • (1991) Biochemistry , vol.30 , pp. 7550-7559
    • Padmanabhan, S.1    Brushaber, V.M.2    Anderson, C.F.3    Record Jr., M.T.4
  • 45
  • 46
    • 0035826988 scopus 로고    scopus 로고
    • Dynamics of collapse of flexible polyelectrolytes in poor solvents
    • Lee N., Thirumalai D. Dynamics of collapse of flexible polyelectrolytes in poor solvents. Macromolecules. 34:2001;3446-3457
    • (2001) Macromolecules , vol.34 , pp. 3446-3457
    • Lee, N.1    Thirumalai, D.2
  • 47
    • 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 D.J., Cech T.R. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure. 9:2001;221-231
    • (2001) Structure , vol.9 , pp. 221-231
    • Juneau, K.1    Podell, E.2    Harrington, D.J.3    Cech, T.R.4


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