메뉴 건너뛰기




Volumn 325, Issue 3, 2003, Pages 421-431

Bistable secondary structures of small RNAs and their structural probing by comparative imino proton NMR spectroscopy

Author keywords

Conformational equilibria; Imino protons; Multistable RNAs; RNA folding; Secondary structure

Indexed keywords

DOUBLE STRANDED RNA;

EID: 0037225166     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01243-3     Document Type: Article
Times cited : (62)

References (48)
  • 2
    • 0031576334 scopus 로고    scopus 로고
    • Folding of RNA involves parallel pathways
    • Pan, J., Thirumalai, D. & Woodson, S. A. (1997). Folding of RNA involves parallel pathways. J. Mol. Biol. 273, 7-13.
    • (1997) J. Mol. Biol. , vol.273 , pp. 7-13
    • Pan, J.1    Thirumalai, D.2    Woodson, S.A.3
  • 3
    • 0036289258 scopus 로고    scopus 로고
    • The folding pathway of genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots
    • Chadalavada, D. M., Senchak, S. E. & Bevilacqua, P. C. (2002). The folding pathway of genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J. Mol. Biol. 317, 559-575.
    • (2002) J. Mol. Biol. , vol.317 , pp. 559-575
    • Chadalavada, D.M.1    Senchak, S.E.2    Bevilacqua, P.C.3
  • 4
    • 0032549735 scopus 로고    scopus 로고
    • Kinetic intermediates trapped by native interactions in RNA folding
    • Treiber, D. K., Rook, M. S., Zarrinkar, P. P. & Williamson, J. R. (1998). Kinetic intermediates trapped by native interactions in RNA folding. Science, 279, 1943-1946.
    • (1998) Science , vol.279 , pp. 1943-1946
    • Treiber, D.K.1    Rook, M.S.2    Zarrinkar, P.P.3    Williamson, J.R.4
  • 5
    • 0032709143 scopus 로고    scopus 로고
    • Metastable structures and refolding kinetics in hok mRNA of plasmid R1
    • Nagel, J. H. A., Gultyaev, A. P., Gerdes, K. & Pleij, C. W. A. (1999). Metastable structures and refolding kinetics in hok mRNA of plasmid R1. RNA, 5, 1408-1419.
    • (1999) RNA , vol.5 , pp. 1408-1419
    • Nagel, J.H.A.1    Gultyaev, A.P.2    Gerdes, K.3    Pleij, C.W.A.4
  • 6
    • 0034698298 scopus 로고    scopus 로고
    • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    • Schultes, E. A. & Bartel, D. P. (2000). One sequence, two ribozymes: Implications for the emergence of new ribozyme folds. Science, 289, 448-452.
    • (2000) Science , vol.289 , pp. 448-452
    • Schultes, E.A.1    Bartel, D.P.2
  • 8
    • 0035280922 scopus 로고    scopus 로고
    • RNA folding transitions and cooperativity
    • Tostesen, E., Chen, S.-J. & Dill, K. A. (2001). RNA folding transitions and cooperativity. J. Phys. Chem. B, 105, 1618-1630.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 1618-1630
    • Tostesen, E.1    Chen, S.-J.2    Dill, K.A.3
  • 9
    • 0037084222 scopus 로고    scopus 로고
    • On RNA two-state conformation equilibria and the impact of nucleobase methylation
    • Höbartner, C., Ebert, M.-O., Jaun, B. & Micura, R. (2002). On RNA two-state conformation equilibria and the impact of nucleobase methylation. Angew. Chem., Int. Ed. Engl. 41, 605-609.
    • (2002) Angew. Chem., Int. Ed. Engl. , vol.41 , pp. 605-609
    • Höbartner, C.1    Ebert, M.-O.2    Jaun, B.3    Micura, R.4
  • 10
    • 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, 11555-11560.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 11555-11560
    • Wu, M.1    Tinoco I., Jr.2
  • 12
    • 0029121733 scopus 로고
    • Exceptionally stable nucleic acid hairpins
    • Varani, G. (1995). Exceptionally stable nucleic acid hairpins. Annu. Rev. Biophys. Biomol. Struct. 24, 397-404.
    • (1995) Annu. Rev. Biophys. Biomol. Struct. , vol.24 , pp. 397-404
    • Varani, G.1
  • 13
    • 0023406843 scopus 로고
    • Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves
    • Marky, L. & Breslauer, K. (1987). Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers, 26, 1601-1620.
    • (1987) Biopolymers , vol.26 , pp. 1601-1620
    • Marky, L.1    Breslauer, K.2
  • 14
    • 0002549050 scopus 로고    scopus 로고
    • Thermodynamics of RNA secondary structure formation
    • (Söll, D., Nishimura, S. & Moore, P., eds), Elsevier, Oxford
    • Xia, T., Mathews, D. H. & Turner, D. H. (1999). Thermodynamics of RNA secondary structure formation. In Comprehensive Natural Product Chemistry (Söll, D., Nishimura, S. & Moore, P., eds), vol. 8, pp. 21-47, Elsevier, Oxford.
    • (1999) Comprehensive Natural Product Chemistry , vol.8 , pp. 21-47
    • Xia, T.1    Mathews, D.H.2    Turner, D.H.3
  • 15
    • 0034744390 scopus 로고    scopus 로고
    • Thermodynamics of 2′-ribose substitutions in UNCG tetraloops
    • Williams, D. J., Boots, J. L. & Hall, K. B. (2001). Thermodynamics of 2′-ribose substitutions in UNCG tetraloops. RNA, 7, 44-53.
    • (2001) RNA , vol.7 , pp. 44-53
    • Williams, D.J.1    Boots, J.L.2    Hall, K.B.3
  • 16
    • 0034193139 scopus 로고    scopus 로고
    • Flexible non-nucleotide linkers as loop replacements in short double helical RNAs
    • Pils, W. & Micura, R. (2000). Flexible non-nucleotide linkers as loop replacements in short double helical RNAs. Nucl. Acids Res. 28, 1859-1863.
    • (2000) Nucl. Acids Res. , vol.28 , pp. 1859-1863
    • Pils, W.1    Micura, R.2
  • 17
    • 0000526813 scopus 로고    scopus 로고
    • Translational control by mRNA structure in eubacteria: Molecular biology and physical chemistry
    • (Simons, R. W. & Grunberg-Manago, M., eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • de Smit, M. H. (1998). Translational control by mRNA structure in eubacteria: Molecular biology and physical chemistry. In RNA Structure and Function (Simons, R. W. & Grunberg-Manago, M., eds), pp. 495-540, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1998) RNA Structure and Function , pp. 495-540
    • De Smit, M.H.1
  • 18
    • 0032900052 scopus 로고    scopus 로고
    • Formation of metastable RNA structures by sequential folding during transcription: Time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis
    • Repsilber, D., Wiese, S., Rachen, M., Schroder, A. W., Riesner, D. & Steger, G. (1999). Formation of metastable RNA structures by sequential folding during transcription: Time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis. RNA, 5, 574-584.
    • (1999) RNA , vol.5 , pp. 574-584
    • Repsilber, D.1    Wiese, S.2    Rachen, M.3    Schroder, A.W.4    Riesner, D.5    Steger, G.6
  • 19
    • 0033198767 scopus 로고    scopus 로고
    • A conformational switch at the 3′-end of a plant virus regulates viral replication
    • Olsthoorn, R. C., Mertens, S., Brederode, F. T. & Bol, J. F. (1999). A conformational switch at the 3′-end of a plant virus regulates viral replication. EMBO J. 18, 4856-4864.
    • (1999) EMBO J. , vol.18 , pp. 4856-4864
    • Olsthoorn, R.C.1    Mertens, S.2    Brederode, F.T.3    Bol, J.F.4
  • 20
    • 0035875554 scopus 로고    scopus 로고
    • Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA
    • Huthoff, H. & Berkhout, B. (2001). Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA. Nucl. Acids Res. 29, 2594-2600.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 2594-2600
    • Huthoff, H.1    Berkhout, B.2
  • 21
    • 0037096843 scopus 로고    scopus 로고
    • Regulated HIV-2 RNA dimerization by means of alternative RNA conformations
    • Dirac, A. M. G., Huthoff, H., Kjems, J. & Berkhout, B. (2002). Regulated HIV-2 RNA dimerization by means of alternative RNA conformations. Nucl. Acids Res. 30, 2647-2655.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 2647-2655
    • Dirac, A.M.G.1    Huthoff, H.2    Kjems, J.3    Berkhout, B.4
  • 22
    • 0028025386 scopus 로고
    • Interaction between acceptor end of tRNA and the T Box stimulates antitermination in the Bacillus subtilis tyrS gene: A new role for the discriminator base
    • Grundy, F. J., Rollins, S. M. & Henkin, T. M. (1994). Interaction between acceptor end of tRNA and the T Box stimulates antitermination in the Bacillus subtilis tyrS gene: A new role for the discriminator base. J. Bacteriol. 176, 4518-4526.
    • (1994) J. Bacteriol. , vol.176 , pp. 4518-4526
    • Grundy, F.J.1    Rollins, S.M.2    Henkin, T.M.3
  • 23
    • 0030806152 scopus 로고    scopus 로고
    • A conformational switch in Escherichia coli 16 S ribosomal RNA during decoding of messenger RNA
    • Lodmell, J. S. & Dahlberg, A. E. (1997). A conformational switch in Escherichia coli 16 S ribosomal RNA during decoding of messenger RNA. Science, 277, 1262-1267.
    • (1997) Science , vol.277 , pp. 1262-1267
    • Lodmell, J.S.1    Dahlberg, A.E.2
  • 24
    • 0030987608 scopus 로고    scopus 로고
    • RNA folding kinetics regulates translation of phage MS2 maturation gene
    • Poot, R. A., Tsareva, N. V., Boni, I. V. & van Duin, J. (1997). RNA folding kinetics regulates translation of phage MS2 maturation gene. Proc. Natl. Acad. Sci. USA, 94, 10110-10115.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 10110-10115
    • Poot, R.A.1    Tsareva, N.V.2    Boni, I.V.3    Van Duin, J.4
  • 25
    • 0035035091 scopus 로고    scopus 로고
    • Translational control by delayed RNA folding: Identification of the kinetic trap
    • van Meerten, D., Girard, G. & van Duin, J. (2001). Translational control by delayed RNA folding: Identification of the kinetic trap. RNA, 7, 483-494.
    • (2001) RNA , vol.7 , pp. 483-494
    • Van Meerten, D.1    Girard, G.2    Van Duin, J.3
  • 26
    • 0031576339 scopus 로고    scopus 로고
    • Programmed cell death by hok/sok of plasmid R1: Coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs
    • Gultyaev, A. P., Franch, T. & Gerdes, K. (1997). Programmed cell death by hok/sok of plasmid R1: Coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs. J. Mol. Biol. 273, 26-37.
    • (1997) J. Mol. Biol. , vol.273 , pp. 26-37
    • Gultyaev, A.P.1    Franch, T.2    Gerdes, K.3
  • 28
    • 2442519939 scopus 로고    scopus 로고
    • Time-resolved fluorescence energy transfer: A versatile tool for the analysis of nucleic acids
    • Klostermeier, D. & Millar, D. P. (2002). Time-resolved fluorescence energy transfer: A versatile tool for the analysis of nucleic acids. Biopolymers, 61, 159-179.
    • (2002) Biopolymers , vol.61 , pp. 159-179
    • Klostermeier, D.1    Millar, D.P.2
  • 29
    • 0034847115 scopus 로고    scopus 로고
    • RNA conformation and folding studied with fluorescence energy transfer
    • Klostermeier, D. & Millar, D. P. (2001). RNA conformation and folding studied with fluorescence energy transfer. Methods, 23, 240-254.
    • (2001) Methods , vol.23 , pp. 240-254
    • Klostermeier, D.1    Millar, D.P.2
  • 30
    • 0034070995 scopus 로고    scopus 로고
    • Calculating nucleic acid secondary structure
    • Zuker, M. (2000). Calculating nucleic acid secondary structure. Curr. Opin. Struct. Biol. 10, 303-310.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 303-310
    • Zuker, M.1
  • 31
    • 0000731155 scopus 로고    scopus 로고
    • Evidence for kinetic effects in folding of large RNA molecules
    • Morgan, S. R. & Higgs, P. G. (1996). Evidence for kinetic effects in folding of large RNA molecules. J. Chem. Phys. 105, 7152-7157.
    • (1996) J. Chem. Phys. , vol.105 , pp. 7152-7157
    • Morgan, S.R.1    Higgs, P.G.2
  • 32
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 34
    • 0030919776 scopus 로고    scopus 로고
    • Prediction of sequentially optimal RNA secondary structures
    • Breton, N., Jacob, C. & Daegelen, P. (1997). Prediction of sequentially optimal RNA secondary structures. J. Biomol. Struct. Dynam. 14, 727-740.
    • (1997) J. Biomol. Struct. Dynam. , vol.14 , pp. 727-740
    • Breton, N.1    Jacob, C.2    Daegelen, P.3
  • 35
    • 0028823370 scopus 로고
    • An interactive framework for RNA secondary structure prediction with a dynamic treatment of constraints
    • Gaspin, C. & Westhof, E. (1995). An interactive framework for RNA secondary structure prediction with a dynamic treatment of constraints. J. Mol. Biol. 254, 163-174.
    • (1995) J. Mol. Biol. , vol.254 , pp. 163-174
    • Gaspin, C.1    Westhof, E.2
  • 36
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty, S., Fontana, W., Hofacker, I. L. & Schuster, P. (1999). Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49, 145-165.
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 37
    • 0034021259 scopus 로고    scopus 로고
    • RNA folding at elementary step resolution
    • Flamm, C., Fontana, W., Hofacker, I. L. & Schuster, P. (2000). RNA folding at elementary step resolution. RNA, 6, 325-338.
    • (2000) RNA , vol.6 , pp. 325-338
    • Flamm, C.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 39
    • 0001884540 scopus 로고    scopus 로고
    • Probing RNA structure and function
    • (Simons, R. W. & Grunberg-Manago, M., eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Moine, H., Ehresmann, B., Ehresmann, C. & Romby, P. (1998). Probing RNA structure and function. In RNA Structure and Function (Simons, R. W. & Grunberg-Manago, M., eds), pp. 77-115, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1998) RNA Structure and Function , pp. 77-115
    • Moine, H.1    Ehresmann, B.2    Ehresmann, C.3    Romby, P.4
  • 40
    • 55949102657 scopus 로고    scopus 로고
    • Chemical and enzymatic methods
    • (Bloomfield, V. A., Crothers, D. A. & Tinoco, I. Jr, eds), University Science Books, Sausalito, CA
    • Hearst, J. (2000). Chemical and enzymatic methods. In Nucleic Acids Structures, Properties, and Function (Bloomfield, V. A., Crothers, D. A. & Tinoco, I. Jr, eds), pp. 45-78, University Science Books, Sausalito, CA.
    • (2000) Nucleic Acids Structures, Properties, and Function , pp. 45-78
    • Hearst, J.1
  • 41
    • 0030031397 scopus 로고    scopus 로고
    • Determining RNA solution structure by segmental isotopic labeling and NMR: Application to Caenorhabtitis elegans spliced leader RNA 1
    • Xu, J., Lapham, J. & Crothers, D. M. (1996). Determining RNA solution structure by segmental isotopic labeling and NMR: Application to Caenorhabtitis elegans spliced leader RNA 1. Proc. Natl. Acad. Sci. USA, 93, 44-48.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 44-48
    • Xu, J.1    Lapham, J.2    Crothers, D.M.3
  • 42
    • 0022542453 scopus 로고
    • NMR evidence for dynamic secondary structure in helices II and III of the 5 S RNA of Escherichia coli
    • Leontis, N. B. & Moore, P. B. (1986). NMR evidence for dynamic secondary structure in helices II and III of the 5 S RNA of Escherichia coli. Biochemistry, 25, 3916-3925.
    • (1986) Biochemistry , vol.25 , pp. 3916-3925
    • Leontis, N.B.1    Moore, P.B.2
  • 43
    • 0025217237 scopus 로고
    • Sequence-dependent structural variations of hammerhead RNA enzymes
    • Heus, H. A., Uhlenbeck, O. C. & Pardi, A. (1990). Sequence-dependent structural variations of hammerhead RNA enzymes. Nucl. Acids Res. 18, 1103-1108.
    • (1990) Nucl. Acids Res. , vol.18 , pp. 1103-1108
    • Heus, H.A.1    Uhlenbeck, O.C.2    Pardi, A.3
  • 44
    • 0025075436 scopus 로고
    • Synthesis and NMR study of ribooligonucleotides forming a hammer-head-type RNA enzyme system
    • Odai, O., Kodama, H., Hiroaki, H., Sakata, T., Tanaka, T. & Uesugi, S. (1990). Synthesis and NMR study of ribooligonucleotides forming a hammer-head-type RNA enzyme system. Nucl. Acids Res. 18, 5955-5960.
    • (1990) Nucl. Acids Res. , vol.18 , pp. 5955-5960
    • Odai, O.1    Kodama, H.2    Hiroaki, H.3    Sakata, T.4    Tanaka, T.5    Uesugi, S.6
  • 45
    • 11544304059 scopus 로고
    • Gaussian pulse cascades: New analytical functions for rectangular selective inversion and in-phase excitation in NMR
    • Emsley, L. & Bodenhausen, G. (1990). Gaussian pulse cascades: New analytical functions for rectangular selective inversion and in-phase excitation in NMR. Chem. Phys. Letters, 165, 469-476.
    • (1990) Chem. Phys. Letters , vol.165 , pp. 469-476
    • Emsley, L.1    Bodenhausen, G.2
  • 46
    • 44949280676 scopus 로고
    • Band-selective radio-frequency pulses
    • Geen, H. & Freeman, R. (1991). Band-selective radio-frequency pulses. J. Magn. Reson. 93, 93-141.
    • (1991) J. Magn. Reson. , vol.93 , pp. 93-141
    • Geen, H.1    Freeman, R.2
  • 48
    • 0002635816 scopus 로고    scopus 로고
    • Conformational changes
    • (Bloomfield, V. A., Crothers, D. M. & Tinoco, I. Jr, eds), University Science Books, Sausalito, CA
    • Turner, D. H. (2000). Conformational changes. In Nucleic Acids (Bloomfield, V. A., Crothers, D. M. & Tinoco, I. Jr, eds), pp. 259-334, University Science Books, Sausalito, CA.
    • (2000) Nucleic Acids , pp. 259-334
    • Turner, D.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.