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Volumn 98, Issue 1, 2010, Pages 111-120

Salt-dependent folding energy landscape of RNA three-way junction

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM; RIBOSOME RNA; SODIUM;

EID: 74049124353     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.09.057     Document Type: Article
Times cited : (14)

References (54)
  • 4
    • 0038508653 scopus 로고    scopus 로고
    • RNA folding: Models and perspectives
    • Sosnick, T. R., and T. Pan. 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
  • 5
    • 16244363320 scopus 로고    scopus 로고
    • Metal ions and RNA folding: A highly charged topic with a dynamic future
    • Woodson, S. A. 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
  • 7
    • 14044271924 scopus 로고    scopus 로고
    • Toroidal DNA condensates: Unraveling the fine structure and the role of nucleation in determining size
    • Hud, N. V., and I. D. Vilfan. 2005. Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size. Annu. Rev. Biophys. Biomol. Struct. 34:295-318.
    • (2005) Annu. Rev. Biophys. Biomol. Struct , vol.34 , pp. 295-318
    • Hud, N.V.1    Vilfan, I.D.2
  • 8
    • 42449155819 scopus 로고    scopus 로고
    • RNA folding: Conformational statistics, folding kinetics, and ion electrostatics
    • Chen, S. J. 2008. RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys. 37:197-214.
    • (2008) Annu Rev Biophys , vol.37 , pp. 197-214
    • Chen, S.J.1
  • 9
    • 33645775325 scopus 로고    scopus 로고
    • Nucleic acid helix stability: Effects of salt concentration, cation valence and size, and chain length
    • Tan, Z. J., and S. J. Chen. 2006. Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys. J. 90:1175-1190.
    • (2006) Biophys. J , vol.90 , pp. 1175-1190
    • Tan, Z.J.1    Chen, S.J.2
  • 11
    • 47749120240 scopus 로고    scopus 로고
    • Salt dependence of nucleic acid hairpin stability
    • Tan, Z. J., and S. J. Chen. 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
  • 12
    • 0035830964 scopus 로고    scopus 로고
    • Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations
    • Heilman-Miller, S. L., D. Thirumalai, and S. A. Woodson. 2001. Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J. Mol. Biol. 306:1157-1166.
    • (2001) J. Mol. Biol , vol.306 , pp. 1157-1166
    • Heilman-Miller, S.L.1    Thirumalai, D.2    Woodson, S.A.3
  • 14
    • 57149093621 scopus 로고    scopus 로고
    • Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations
    • Qiu, X., K. Andresen, ..., L. Pollack. 2008. Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations. Phys. Rev. Lett. 101:228101.
    • (2008) Phys. Rev. Lett , vol.101 , pp. 228101
    • Qiu, X.1    Andresen, K.2    Pollack, L.3
  • 15
    • 4444370899 scopus 로고    scopus 로고
    • Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme
    • Shcherbakova, I., S. Gupta, ..., M. Brenowitz. 2004. Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J. Mol. Biol. 342:1431-1442.
    • (2004) J. Mol. Biol , vol.342 , pp. 1431-1442
    • Shcherbakova, I.1    Gupta, S.2    Brenowitz, M.3
  • 16
    • 0033636685 scopus 로고    scopus 로고
    • Structures of helical junctions in nucleic acids
    • Lilley, D. M. 2000. Structures of helical junctions in nucleic acids. Q. Rev. Biophys. 33:109-159.
    • (2000) Q. Rev. Biophys , vol.33 , pp. 109-159
    • Lilley, D.M.1
  • 17
    • 20444502087 scopus 로고    scopus 로고
    • Structure, folding and mechanisms of ribozymes
    • Lilley, D. M. 2005. Structure, folding and mechanisms of ribozymes. Curr. Opin. Struct. Biol. 15:313-323.
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 313-323
    • Lilley, D.M.1
  • 18
    • 0042925420 scopus 로고    scopus 로고
    • Single-molecule transition-state analysis of RNA folding
    • Bokinsky, G., D. Rueda, ..., X. Zhuang. 2003. Single-molecule transition-state analysis of RNA folding. Proc. Natl. Acad. Sci. USA. 100:9302-9307.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9302-9307
    • Bokinsky, G.1    Rueda, D.2    Zhuang, X.3
  • 19
    • 0031856886 scopus 로고    scopus 로고
    • Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15
    • Batey, R. T., and J. R. Williamson. 1998. Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15. RNA. 4:984-997.
    • (1998) RNA , vol.4 , pp. 984-997
    • Batey, R.T.1    Williamson, J.R.2
  • 20
    • 0032559410 scopus 로고    scopus 로고
    • 2+)-induced conformational changes in the S15 binding site of 16 S ribosomal RNA
    • 2+)-induced conformational changes in the S15 binding site of 16 S ribosomal RNA. J. Mol. Biol. 275:453-464.
    • (1998) J. Mol. Biol , vol.275 , pp. 453-464
    • Orr, J.W.1    Hagerman, P.J.2    Williamson, J.R.3
  • 21
    • 2542601493 scopus 로고    scopus 로고
    • A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly
    • Klostermeier, D., P. Sears, ..., J. R. Williamson. 2004. A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly. Nucleic Acids Res. 32:2707-2715.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2707-2715
    • Klostermeier, D.1    Sears, P.2    Williamson, J.R.3
  • 22
    • 0037006790 scopus 로고    scopus 로고
    • 2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules
    • 2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc. Natl. Acad. Sci. USA. 99:4284-4289.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 4284-4289
    • Kim, H.D.1    Nienhaus, G.U.2    Chu, S.3
  • 23
    • 0033529972 scopus 로고    scopus 로고
    • Ligand-induced conformational changes observed in single RNA molecules
    • Ha, T., X. Zhuang, ..., S. Chu. 1999. Ligand-induced conformational changes observed in single RNA molecules. Proc. Natl. Acad. Sci. USA. 96:9077-9082.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9077-9082
    • Ha, T.1    Zhuang, X.2    Chu, S.3
  • 24
    • 44349144363 scopus 로고    scopus 로고
    • 2+-concentration jump experiments reveal details of the early folding pathways of a large RNA
    • 2+-concentration jump experiments reveal details of the early folding pathways of a large RNA. Proc. Natl. Acad. Sci. USA. 105:6602-6607.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 6602-6607
    • Qu, X.1    Smith, G.J.2    Scherer, N.F.3
  • 25
    • 28144441819 scopus 로고    scopus 로고
    • Ion atmosphere of three-way junction nucleic acid
    • Mohanty, U., A. Spasic, ..., S. Chu. 2005. Ion atmosphere of three-way junction nucleic acid. J. Phys. Chem. B. 109:21369-21374.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 21369-21374
    • Mohanty, U.1    Spasic, A.2    Chu, S.3
  • 26
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning, G. S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 2:179-246.
    • (1978) Q. Rev. Biophys , vol.2 , pp. 179-246
    • Manning, G.S.1
  • 27
    • 45749159088 scopus 로고    scopus 로고
    • Counterion condensation in nucleic acid
    • Alex, S., and U. Mohanty. 2007. Counterion condensation in nucleic acid. Adv. Chem. Phys. 139:139-176.
    • (2007) Adv. Chem. Phys , vol.139 , pp. 139-176
    • Alex, S.1    Mohanty, U.2
  • 28
    • 0032563745 scopus 로고    scopus 로고
    • Excess counterion binding and ionic stability of kinked and branched DNA
    • Fenley, M. O., G. S. Manning, ..., W. K. Olson. 1998. Excess counterion binding and ionic stability of kinked and branched DNA. Biophys. Chem. 74:135-152.
    • (1998) Biophys. Chem , vol.74 , pp. 135-152
    • Fenley, M.O.1    Manning, G.S.2    Olson, W.K.3
  • 29
    • 0031354944 scopus 로고    scopus 로고
    • Counterion condensation on ionic oligomers
    • Manning, G. S., and U. Mohanty. 1997. Counterion condensation on ionic oligomers. Physica A. 247:196-204.
    • (1997) Physica A , vol.247 , pp. 196-204
    • Manning, G.S.1    Mohanty, U.2
  • 30
    • 33947707250 scopus 로고    scopus 로고
    • A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation
    • Boschitsch, A. H., and M. O. Fenley. 2007. A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation. J. Comput. Chem. 28:909-921.
    • (2007) J. Comput. Chem , vol.28 , pp. 909-921
    • Boschitsch, A.H.1    Fenley, M.O.2
  • 31
    • 20444458780 scopus 로고    scopus 로고
    • +) accumulation and anion (X-) exclusion in mixed salt solutions of polyanionic DNA using Monte Carlo and Poisson-Boltzmann calculations of ion-polyion preferential interaction coefficients
    • +) accumulation and anion (X-) exclusion in mixed salt solutions of polyanionic DNA using Monte Carlo and Poisson-Boltzmann calculations of ion-polyion preferential interaction coefficients. J. Phys. Chem. B. 103:3489-3504.
    • (1999) J. Phys. Chem. B , vol.103 , pp. 3489-3504
    • Ni, H.H.1    Anderson, C.F.2    Record, M.T.3
  • 32
    • 51949119253 scopus 로고    scopus 로고
    • Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble
    • Bai, Y. V. B., V. B. Chu, ..., S. Doniach. 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.V.B.1    Chu, V.B.2    Doniach, S.3
  • 33
    • 34249814641 scopus 로고    scopus 로고
    • Dielectric saturation of the ion hydration shell and interaction between two double helices of DNA in mono- and multivalent electrolyte solutions: Foundations of the ε-modified Poisson-Boltzmann theory
    • Gavryushov, S. 2007. Dielectric saturation of the ion hydration shell and interaction between two double helices of DNA in mono- and multivalent electrolyte solutions: foundations of the ε-modified Poisson-Boltzmann theory. J. Phys. Chem. B. 111:5264-5276.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 5264-5276
    • Gavryushov, S.1
  • 34
    • 43949124153 scopus 로고    scopus 로고
    • Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model
    • Wang, K., Y.-X. Yu, and G.-H. Gao. 2008. Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model. J. Chem. Phys. 128:185101.
    • (2008) J. Chem. Phys , vol.128 , pp. 185101
    • Wang, K.1    Yu, Y.-X.2    Gao, G.-H.3
  • 35
    • 16244384381 scopus 로고    scopus 로고
    • Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte
    • Tan, Z. J., and S.-J. Chen. 2005. Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. J. Chem. Phys. 122:044903.
    • (2005) J. Chem. Phys , vol.122 , pp. 044903
    • Tan, Z.J.1    Chen, S.-J.2
  • 36
    • 36449001060 scopus 로고
    • Ionic distribution around simple DNA models. I. Cylindrically averaged properties
    • Montoro, J. C. G., and J. L. F. Abascal. 1995. Ionic distribution around simple DNA models. I. Cylindrically averaged properties. J. Chem. Phys. 103:8273-8284.
    • (1995) J. Chem. Phys , vol.103 , pp. 8273-8284
    • Montoro, J.C.G.1    Abascal, J.L.F.2
  • 37
    • 0034036031 scopus 로고    scopus 로고
    • Crystal structure of the S15-rRNA complex
    • Nikulin, A., A. Serganov, ..., P. Dumas. 2000. Crystal structure of the S15-rRNA complex. Nat. Struct. Biol. 7:273-277.
    • (2000) Nat. Struct. Biol , vol.7 , pp. 273-277
    • Nikulin, A.1    Serganov, A.2    Dumas, P.3
  • 38
    • 43149107203 scopus 로고    scopus 로고
    • Electrostatic free energy landscapes for DNA helix bending
    • Tan, Z. J., and S. J. Chen. 2008. Electrostatic free energy landscapes for DNA helix bending. Biophys. J. 94:3137-3149.
    • (2008) Biophys. J , vol.94 , pp. 3137-3149
    • Tan, Z.J.1    Chen, S.J.2
  • 39
    • 33745728321 scopus 로고    scopus 로고
    • Ion-mediated nucleic acid helix-helix interactions
    • Tan, Z. J., and S. J. Chen. 2006. Ion-mediated nucleic acid helix-helix interactions. Biophys. J. 91:518-536.
    • (2006) Biophys. J , vol.91 , pp. 518-536
    • Tan, Z.J.1    Chen, S.J.2
  • 40
    • 0028143014 scopus 로고
    • Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
    • Walter, A. E., and D. H. Turner. 1994. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry. 33:12715-12719.
    • (1994) Biochemistry , vol.33 , pp. 12715-12719
    • Walter, A.E.1    Turner, D.H.2
  • 41
    • 44849088283 scopus 로고    scopus 로고
    • Li, L., S. A. Pabit, ..., L. Pollack. 2008. Closing the lid on DNA end-toend stacking interactions. Appl. Phys. Lett. 92:223901-2239013.
    • Li, L., S. A. Pabit, ..., L. Pollack. 2008. Closing the lid on DNA end-toend stacking interactions. Appl. Phys. Lett. 92:223901-2239013.
  • 42
    • 36848999901 scopus 로고    scopus 로고
    • Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
    • Bai, Y., M. Greenfeld, ..., D. Herschlag. 2007. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J. Am. Chem. Soc. 129:14981-14988.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 14981-14988
    • Bai, Y.1    Greenfeld, M.2    Herschlag, D.3
  • 43
    • 33845906906 scopus 로고    scopus 로고
    • Electrostatic free energy landscapes for nucleic acid helix assembly
    • Tan, Z. J., and S.-J. Chen. 2006. Electrostatic free energy landscapes for nucleic acid helix assembly. Nucleic Acids Res. 34:6629-6639.
    • (2006) Nucleic Acids Res , vol.34 , pp. 6629-6639
    • Tan, Z.J.1    Chen, S.-J.2
  • 44
    • 33847682251 scopus 로고    scopus 로고
    • Charge density of divalent metal cations determines RNA stability
    • Koculi, E., C. Hyeon, ..., S. A. Woodson. 2007. Charge density of divalent metal cations determines RNA stability. J. Am. Chem. Soc. 129:2676-2682.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 2676-2682
    • Koculi, E.1    Hyeon, C.2    Woodson, S.A.3
  • 45
    • 36048952831 scopus 로고    scopus 로고
    • Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory
    • Chu, V. B., Y. Bai, ..., S. Doniach. 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    Doniach, S.3
  • 46
    • 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
  • 47
    • 42749101028 scopus 로고    scopus 로고
    • Spatial distribution of competing ions around DNA in solution
    • Andresen, K., R. Das, ..., L. Pollack. 2004. Spatial distribution of competing ions around DNA in solution. Phys. Rev. Lett. 93:248103.
    • (2004) Phys. Rev. Lett , vol.93 , pp. 248103
    • Andresen, K.1    Das, R.2    Pollack, L.3
  • 48
    • 0036816641 scopus 로고    scopus 로고
    • Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting
    • Brenowitz, M., M. R. Chance, ..., K. Takamoto. 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    Takamoto, K.3
  • 49
    • 33847028397 scopus 로고    scopus 로고
    • Quantitative analysis of monovalent counterion binding to random-sequence, doublestranded DNA using the replacement ion method
    • Stellwagen, E., Q. Dong, and N. C. Stellwagen. 2007. Quantitative analysis of monovalent counterion binding to random-sequence, doublestranded DNA using the replacement ion method. Biochemistry. 46:2050-2058.
    • (2007) Biochemistry , vol.46 , pp. 2050-2058
    • Stellwagen, E.1    Dong, Q.2    Stellwagen, N.C.3
  • 50
    • 41449101436 scopus 로고    scopus 로고
    • Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts
    • Lu, Y., and N. C. Stellwagen. 2008. Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts. Biophys. J. 94:1719-1725.
    • (2008) Biophys. J , vol.94 , pp. 1719-1725
    • Lu, Y.1    Stellwagen, N.C.2
  • 51
    • 0026558204 scopus 로고
    • Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces
    • Rau, D. C., and V. A. Parsegian. 1992. Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces. Biophys. J. 61:246-259.
    • (1992) Biophys. J , vol.61 , pp. 246-259
    • Rau, D.C.1    Parsegian, V.A.2
  • 52
    • 12844260994 scopus 로고    scopus 로고
    • Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
    • Bai, Y., R. Das, ..., S. Doniach. 2005. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc. Natl. Acad. Sci. USA. 102:1035-1040.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 1035-1040
    • Bai, Y.1    Das, R.2    Doniach, S.3
  • 54
    • 0027398505 scopus 로고
    • Metal ion catalysis in the Tetrahymena ribozyme reaction
    • Piccirilli, J. A., J. S. Vyle, ..., T. R. Cech. 1993. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature. 361:85-88.
    • (1993) Nature , vol.361 , pp. 85-88
    • Piccirilli, J.A.1    Vyle, J.S.2    Cech, T.R.3


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