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Volumn 30, Issue 21, 2002, Pages 4751-4760

Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM ION; NUCLEOSIDE; PHENYLALANINE; TRANSFER RNA;

EID: 0036848383     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf595     Document Type: Article
Times cited : (64)

References (59)
  • 2
    • 0016849405 scopus 로고
    • Genetic perturbations that reveal tertiary conformation of tRNA precursor molecules
    • McClain, W.H. and Seidman, J.G. (1975) Genetic perturbations that reveal tertiary conformation of tRNA precursor molecules. Nature, 257, 106-110.
    • (1975) Nature , vol.257 , pp. 106-110
    • McClain, W.H.1    Seidman, J.G.2
  • 3
    • 0002495140 scopus 로고
    • Biosynthesis and function of modified nucleosides
    • Soll, D. and RajBhandary, U.L. (eds), ASM, Washington DC
    • Bjork, G.R. (1995) Biosynthesis and function of modified nucleosides. In Soll, D. and RajBhandary, U.L. (eds), tRNA: Structure, Biosynthesis and Function. ASM, Washington DC, pp. 165-205.
    • (1995) TRNA: Structure, Biosynthesis and Function , pp. 165-205
    • Bjork, G.R.1
  • 4
    • 0015929511 scopus 로고
    • Three-dimensional structure of yeast phenylalanine transfer RNA: Folding of the polynucleotide chain
    • Kim, S.H., Quigley, G.J., Suddath, F.L., McPherson, A., Sneden, D., Kim, J.J., Weinzierl, J. and Rich, A. (1973) Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain. Science, 179, 285-288.
    • (1973) Science , vol.179 , pp. 285-288
    • Kim, S.H.1    Quigley, G.J.2    Suddath, F.L.3    McPherson, A.4    Sneden, D.5    Kim, J.J.6    Weinzierl, J.7    Rich, A.8
  • 5
    • 0025726470 scopus 로고
    • The T-arm of tRNA is a substrate for tRNA (m5U54)-methyltransferase
    • Gu, X.R. and Santi, D.V. (1991) The T-arm of tRNA is a substrate for tRNA (m5U54)-methyltransferase. Biochemistry, 30, 2999-3002.
    • (1991) Biochemistry , vol.30 , pp. 2999-3002
    • Gu, X.R.1    Santi, D.V.2
  • 6
    • 0032488604 scopus 로고    scopus 로고
    • Molecular recognition of tRNA by tRNA pseudouridine 55 synthase
    • Gu, X., Yu, M., Ivanetick, K.M. and Santi, D.V. (1998) Molecular recognition of tRNA by tRNA pseudouridine 55 synthase. Biochemistry, 37, 339-343.
    • (1998) Biochemistry , vol.37 , pp. 339-343
    • Gu, X.1    Yu, M.2    Ivanetick, K.M.3    Santi, D.V.4
  • 7
    • 0034653278 scopus 로고    scopus 로고
    • Modified constructs of the tRNA TΨC domain to probe substrate conformational requirements of m(1)A(58) and m(5)U(54) tRNA methyltransferases
    • Sengupta, S., Saulius, V., Yarian, C., Sochacka, E., Malkiewicz, A., Guenther, R., Koshlap, K.M. and Agris, P.F. (2000) Modified constructs of the tRNA TΨC domain to probe substrate conformational requirements of m(1)A(58) and m(5)U(54) tRNA methyltransferases. Nucleic Acids Res., 28, 1374-1380.
    • (2000) Nucleic Acids Res , vol.28 , pp. 1374-1380
    • Sengupta, S.1    Saulius, V.2    Yarian, C.3    Sochacka, E.4    Malkiewicz, A.5    Guenther, R.6    Koshlap, K.M.7    Agris, P.F.8
  • 9
    • 0034547125 scopus 로고    scopus 로고
    • Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells
    • Gutgsell, N., Englund, N., Niu, L., Kaya, Y., Lane, B.G. and Ofengand, J. (2000) Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells. RNA, 6, 1870-1881.
    • (2000) RNA , vol.6 , pp. 1870-1881
    • Gutgsell, N.1    Englund, N.2    Niu, L.3    Kaya, Y.4    Lane, B.G.5    Ofengand, J.6
  • 11
    • 0036226647 scopus 로고    scopus 로고
    • 54)-methyltransferase in tRNA maturation
    • 54)-methyltransferase in tRNA maturation. RNA, 8, 324-335.
    • (2002) RNA , vol.8 , pp. 324-335
    • Johansson, M.J.O.1    Byström, A.S.2
  • 12
    • 0032542064 scopus 로고    scopus 로고
    • Conformational transitions of an unmodified tRNA: Implications for RNA folding
    • Maglott, E.J., Deo, S.S., Przykorska, A. and Glick, G.D. (1998) Conformational transitions of an unmodified tRNA: implications for RNA folding. Biochemistry, 37, 16349-16359.
    • (1998) Biochemistry , vol.37 , pp. 16349-16359
    • Maglott, E.J.1    Deo, S.S.2    Przykorska, A.3    Glick, G.D.4
  • 14
    • 0033592945 scopus 로고    scopus 로고
    • Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding
    • Shelton, V.M., Sosnick, T.R. and Pan, T. (1999) Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry, 38, 16831-16839.
    • (1999) Biochemistry , vol.38 , pp. 16831-16839
    • Shelton, V.M.1    Sosnick, T.R.2    Pan, T.3
  • 18
    • 0033534387 scopus 로고    scopus 로고
    • Lys,3 by an A+-C base-pair and by pseudouridine
    • Lys,3 by an A+-C base-pair and by pseudouridine. J. Mol. Biol., 285, 115-131.
    • (1999) J. Mol. Biol , vol.285 , pp. 115-131
    • Durant, P.C.1    Davis, D.R.2
  • 19
    • 0032617148 scopus 로고    scopus 로고
    • Thermodynamic contribution of nucleoside modifications to yeast tRNA(Phe) anticodon stem loop analogs
    • Agris, P.F., Guenther, R., Sochacka, E., Newman, W., Czerwinska, G. and Malkiewicz, A. (1999) Thermodynamic contribution of nucleoside modifications to yeast tRNA(Phe) anticodon stem loop analogs. Acta Biochim. Pol, 46, 163-172.
    • (1999) Acta Biochim. Pol , vol.46 , pp. 163-172
    • Agris, P.F.1    Guenther, R.2    Sochacka, E.3    Newman, W.4    Czerwinska, G.5    Malkiewicz, A.6
  • 21
    • 0018462013 scopus 로고
    • Role of ribothymidine in the thermal stability of transfer RNA as monitored by proton magnetic resonance
    • Davanloo, P., Sprinzl, M., Watanabe, K., Albani, M. and Kersten, H. (1979) Role of ribothymidine in the thermal stability of transfer RNA as monitored by proton magnetic resonance. Nucleic Acids Res., 6, 1571-1581.
    • (1979) Nucleic Acids Res , vol.6 , pp. 1571-1581
    • Davanloo, P.1    Sprinzl, M.2    Watanabe, K.3    Albani, M.4    Kersten, H.5
  • 22
    • 0031113361 scopus 로고    scopus 로고
    • The dynamic NMR structure of the TΨC-loop: Implications for the specificity of tRNA methylation
    • Yao, L.J., James, T.L., Kealey, J.T., Santi, D.V. and Schmitz, U. (1997) The dynamic NMR structure of the TΨC-loop: implications for the specificity of tRNA methylation. J. Biomol. NMR, 9, 229-244.
    • (1997) J. Biomol. NMR , vol.9 , pp. 229-244
    • Yao, L.J.1    James, T.L.2    Kealey, J.T.3    Santi, D.V.4    Schmitz, U.5
  • 23
    • 0032189738 scopus 로고    scopus 로고
    • Small structural ensembles for a 17-nucleotide mimic of the tRNA TΨC-loop via fitting dipolar relaxation rates with the quadratic programming algorithm
    • Schmitz, U., Donati, A., James, T.L., Ulyanov, N.B. and Yao, L. (1998) Small structural ensembles for a 17-nucleotide mimic of the tRNA TΨC-loop via fitting dipolar relaxation rates with the quadratic programming algorithm. Biopolymers, 46, 329-342.
    • (1998) Biopolymers , vol.46 , pp. 329-342
    • Schmitz, U.1    Donati, A.2    James, T.L.3    Ulyanov, N.B.4    Yao, L.5
  • 25
    • 0034625314 scopus 로고    scopus 로고
    • (2+) binding to tRNA revisited: The nonlinear Poisson-Boltzmarm model
    • (2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmarm model. J. Mol. Biol. 299, 813-825.
    • (2000) J. Mol. Biol , vol.299 , pp. 813-825
    • Misra, V.K.1    Draper, D.E.2
  • 26
    • 0033862354 scopus 로고    scopus 로고
    • The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited
    • Shi, H. and Moore, P.B. (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA, 6, 1091-1105.
    • (2000) RNA , vol.6 , pp. 1091-1105
    • Shi, H.1    Moore, P.B.2
  • 31
    • 0034840624 scopus 로고    scopus 로고
    • RNA oligonucleotide synthesis via 5′-silyl-2′-orthoester chemistry
    • Scaringe, S.A. (2001) RNA oligonucleotide synthesis via 5′-silyl-2′-orthoester chemistry. Methods, 23, 206-217.
    • (2001) Methods , vol.23 , pp. 206-217
    • Scaringe, S.A.1
  • 32
    • 0032884788 scopus 로고    scopus 로고
    • Fast and reliable automated synthesis of RNA and partially 2′-O-protected precursors ('Caged RNA') based on two novel, orthogonal 2′-O-protecting groups
    • Pitsch, S., Weiss, P.A., Wu, X., Ackermann, D. and Honegger, T. (1999) Fast and reliable automated synthesis of RNA and partially 2′-O-protected precursors ('Caged RNA') based on two novel, orthogonal 2′-O-protecting groups. Helv. Chim. Acta, 82, 1753-1761.
    • (1999) Helv. Chim. Acta , vol.82 , pp. 1753-1761
    • Pitsch, S.1    Weiss, P.A.2    Wu, X.3    Ackermann, D.4    Honegger, T.5
  • 33
    • 0006021423 scopus 로고
    • Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity
    • Ogilvie, K.K., Usman, N., Nicoghosian, K. and Cedergren, R.J. (1988) Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity. Proc. Natl Acad. Sci. USA, 85, 5764-5768.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 5764-5768
    • Ogilvie, K.K.1    Usman, N.2    Nicoghosian, K.3    Cedergren, R.J.4
  • 34
    • 0028915734 scopus 로고
    • Site-selected introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry
    • Agris, P.F., Malkiewicz, A., Kraszewski, A., Everett, K., Nawrot, B., Sochacka, E., Jankowska, J. and Guenther, R. (1995) Site-selected introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry. Biochimie, 77, 125-34.
    • (1995) Biochimie , vol.77 , pp. 125-134
    • Agris, P.F.1    Malkiewicz, A.2    Kraszewski, A.3    Everett, K.4    Nawrot, B.5    Sochacka, E.6    Jankowska, J.7    Guenther, R.8
  • 35
    • 0018120558 scopus 로고
    • 3′-terminal labelling of RNA with T4 RNA ligase
    • England, T.E. and Uhlenbeck, O.C. (1978) 3′-terminal labelling of RNA with T4 RNA ligase. Nature, 275, 560-561.
    • (1978) Nature , vol.275 , pp. 560-561
    • England, T.E.1    Uhlenbeck, O.C.2
  • 36
    • 0025336478 scopus 로고
    • Autoradiography using storage phosphor technology
    • Johnston, R.J., Pickett, S.C. and Barker, D.L. (1990) Autoradiography using storage phosphor technology. Electrophoresis, 11, 355-360.
    • (1990) Electrophoresis , vol.11 , pp. 355-360
    • Johnston, R.J.1    Pickett, S.C.2    Barker, D.L.3
  • 37
    • 0026439857 scopus 로고
    • Catalytic RNA reactions of yeast tRNA(Phe) fragments
    • Deng, H.Y. and Termini, J. (1992) Catalytic RNA reactions of yeast tRNA(Phe) fragments. Biochemistry, 31, 10518-10528.
    • (1992) Biochemistry , vol.31 , pp. 10518-10528
    • Deng, H.Y.1    Termini, J.2
  • 38
    • 0033543603 scopus 로고    scopus 로고
    • Sequence-dependent conformational differences of small RNAs as revealed by native gel electrophoresis
    • Beuning, P.J., Tessmer, M.R., Baumann, C.G., Kallick, D.A. and Musier-Forzyth, K. (1999) Sequence-dependent conformational differences of small RNAs as revealed by native gel electrophoresis. Anal. Biochem., 273, 284-290.
    • (1999) Anal. Biochem , vol.273 , pp. 284-290
    • Beuning, P.J.1    Tessmer, M.R.2    Baumann, C.G.3    Kallick, D.A.4    Musier-Forzyth, K.5
  • 39
    • 0035544790 scopus 로고    scopus 로고
    • Structural changes of tRNA and 5S rRNA induced with magnesium and visualized with synchrotron mediated hydroxyl radical cleavage
    • Barciszewska, M.Z., Rapp, G., Betzel. C., Erdmann,V.A. and Barciszewski, J. (2001) Structural changes of tRNA and 5S rRNA induced with magnesium and visualized with synchrotron mediated hydroxyl radical cleavage. Mol. Biol. Rep., 28, 103-110.
    • (2001) Mol. Biol. Rep , vol.28 , pp. 103-110
    • Barciszewska, M.Z.1    Rapp, G.2    Betzel, C.3    Erdmann, V.A.4    Barcoszewska, J.5
  • 40
    • 0014688034 scopus 로고
    • Detailed molecular model for transfer ribonucleic acid
    • Levitt, M. (1969) Detailed molecular model for transfer ribonucleic acid. Nature 224, 759-763.
    • (1969) Nature , vol.224 , pp. 759-763
    • Levitt, M.1
  • 44
    • 0016588225 scopus 로고
    • Tertiary structure of tRNAPhe (yeast): Kinetics and electrostatic repulsion
    • Urbanke, C., Romer, R. and Maass, G. (1975) Tertiary structure of tRNAPhe (yeast): kinetics and electrostatic repulsion. Eur. J. Biochem., 55, 439-444.
    • (1975) Eur. J. Biochem , vol.55 , pp. 439-444
    • Urbanke, C.1    Romer, R.2    Maass, G.3
  • 45
    • 0036224052 scopus 로고    scopus 로고
    • Effects of magnesium ions on the stabilization of RNA oligomers of defined structures
    • Serra, M.J., Baird, J.D., Dale, T., Fey, B.L., Retatagos, K. and Westhof, E. (2002) Effects of magnesium ions on the stabilization of RNA oligomers of defined structures. RNA, 8, 307-323.
    • (2002) RNA , vol.8 , pp. 307-323
    • Serra, M.J.1    Baird, J.D.2    Dale, T.3    Fey, B.L.4    Retatagos, K.5    Westhof, E.6
  • 46
    • 0034104321 scopus 로고    scopus 로고
    • Compact but disordered states of RNA
    • Woodson, S.A. (2000) Compact but disordered states of RNA. Nature Struct. Biol., 7, 349-352.
    • (2000) Nature Struct. Biol , vol.7 , pp. 349-352
    • Woodson, S.A.1
  • 48
    • 0032578472 scopus 로고    scopus 로고
    • RNA folding causes secondary structure rearrangement
    • Wu, M. and 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
  • 49
    • 0015497428 scopus 로고
    • Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli)
    • Cole, P.E. and Crothers, D.M. (1972) Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli). Biochemistry, 11, 4368-4374.
    • (1972) Biochemistry , vol.11 , pp. 4368-4374
    • Cole, P.E.1    Crothers, D.M.2
  • 50
    • 0015848275 scopus 로고
    • The conformational transitions in yeast tRNAPhe as studied with tRNAPhe fragments
    • Riesner, D., Maass, G., Thiebe, R., Philippsen, P. and Zachau, H.G. (1973) The conformational transitions in yeast tRNAPhe as studied with tRNAPhe fragments. Eur. J. Biochem., 36, 76-88.
    • (1973) Eur. J. Biochem , vol.36 , pp. 76-88
    • Riesner, D.1    Maass, G.2    Thiebe, R.3    Philippsen, P.4    Zachau, H.G.5
  • 51
    • 0034059197 scopus 로고    scopus 로고
    • Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation
    • Ralston, C.Y., He, Q., Brenowitz, M. and Chance, M.R. (2000) Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation. Nature Struct. Biol., 7, 371-374.
    • (2000) Nature Struct. Biol , vol.7 , pp. 371-374
    • Ralston, C.Y.1    He, Q.2    Brenowitz, M.3    Chance, M.R.4
  • 52
    • 0035906731 scopus 로고    scopus 로고
    • Probing the folding landscape of the Tetrahymena ribozyme: Commitment to form the native conformation is late in the folding pathway
    • Russell, R. and Herschlag, D. (2001) Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. J. Mol. Biol., 308, 839-851.
    • (2001) J. Mol. Biol , vol.308 , pp. 839-851
    • Russell, R.1    Herschlag, D.2
  • 54
    • 0034657608 scopus 로고    scopus 로고
    • Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA
    • Meroueh, M., Grohar, P.J., Qiu, J., SantaLucia, J.,Jr, Scaringe, S.A. and Chow, C.S. (2000) Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA. Nucleic Acids Res., 28, 2075-2083.
    • (2000) Nucleic Acids Res , vol.28 , pp. 2075-2083
    • Meroueh, M.1    Grohar, P.J.2    Qiu, J.3    SantaLucia J., Jr.4    Scaringe, S.A.5    Chow, C.S.6
  • 55
    • 0034975454 scopus 로고    scopus 로고
    • A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture
    • Newby, M.I. and Greenbaum, N.L. (2001) A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture. RNA, 7, 833-845.
    • (2001) RNA , vol.7 , pp. 833-845
    • Newby, M.I.1    Greenbaum, N.L.2
  • 56
    • 0036295964 scopus 로고    scopus 로고
    • The linkage between magnesium binding and RNA folding
    • Misra, V.K. and Draper, D.E. (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
  • 58
    • 0034547125 scopus 로고    scopus 로고
    • Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells
    • Gutgsell, N., England, N., Niu, L., Kaya, Y., Lane, B.G. and Ofengand, J. (2000) Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells. RNA, 6, 1870-1881.
    • (2000) RNA , vol.6 , pp. 1870-1881
    • Gutgsell, N.1    England, N.2    Niu, L.3    Kaya, Y.4    Lane, B.G.5    Ofengand, J.6


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