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Volumn 5, Issue 4, 1999, Pages 574-584

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

Author keywords

Kinetics; Rate of transcription; RNA secondary structure; Structure formation

Indexed keywords

DNA DIRECTED RNA POLYMERASE;

EID: 0032900052     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299982018     Document Type: Article
Times cited : (76)

References (43)
  • 1
    • 0020740241 scopus 로고
    • Analysis of numerical methods for computer simulation of kinetic processes: Development of KINSIM - A flexible, portable system
    • Barshop BA, Wrenn RF, Frieden C. 1983. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM - a flexible, portable system. Anal Biochem 130:134-145.
    • (1983) Anal Biochem , vol.130 , pp. 134-145
    • Barshop, B.A.1    Wrenn, R.F.2    Frieden, C.3
  • 2
    • 0028892438 scopus 로고
    • Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract
    • Baumstark T, Riesner D. 1995. Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract. Nucleic Acids Res 23:4246-4254.
    • (1995) Nucleic Acids Res , vol.23 , pp. 4246-4254
    • Baumstark, T.1    Riesner, D.2
  • 3
    • 19244375613 scopus 로고    scopus 로고
    • Viroid processing: Switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation
    • Baumstark T, Schröder AR, Riesner D. 1997. Viroid processing: Switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation. EMBO J 16:599-610.
    • (1997) EMBO J , vol.16 , pp. 599-610
    • Baumstark, T.1    Schröder, A.R.2    Riesner, D.3
  • 4
    • 84982740386 scopus 로고
    • Fatal yellowing of oil palms: Search for viroids and double-stranded RNA
    • Beuther E, Wiese U, Lukács N, van Slobbe WG, Riesner D. 1992. Fatal yellowing of oil palms: Search for viroids and double-stranded RNA. J Phytopath 136:297-311.
    • (1992) J Phytopath , vol.136 , pp. 297-311
    • Beuther, E.1    Wiese, U.2    Lukács, N.3    Van Slobbe, W.G.4    Riesner, D.5
  • 5
    • 0019317307 scopus 로고
    • Sequential folding of transfer RNA: A nuclear magnetic resonance study of successively longer tRNA fragments with a common 5′ end
    • Boyle J, Robillard GT, Kim SH. 1980. Sequential folding of transfer RNA: A nuclear magnetic resonance study of successively longer tRNA fragments with a common 5′ end. J Mol Biol 139:601-625.
    • (1980) J Mol Biol , vol.139 , pp. 601-625
    • Boyle, J.1    Robillard, G.T.2    Kim, S.H.3
  • 6
    • 0015935359 scopus 로고
    • Characterization of T7-specific ribonucleic acid polymerase. I. General properties of the enzymatic reaction and the template specificity of the enzyme
    • Chamberlin M, Ring J. 1973. Characterization of T7-specific ribonucleic acid polymerase. I. General properties of the enzymatic reaction and the template specificity of the enzyme. J Biol Chem 248:2235-2244.
    • (1973) J Biol Chem , vol.248 , pp. 2235-2244
    • Chamberlin, M.1    Ring, J.2
  • 7
    • 0029003103 scopus 로고
    • RNAII transcribed by IPTG-induced T7 RNA polymerase is non-functional as a replication primer for ColE1-type plasmids in Escherichia coli
    • Chao MY, Kan MC, Lin-Chao S. 1995. RNAII transcribed by IPTG-induced T7 RNA polymerase is non-functional as a replication primer for ColE1-type plasmids in Escherichia coli. Nucleic Acids Res 23:1691-1695.
    • (1995) Nucleic Acids Res , vol.23 , pp. 1691-1695
    • Chao, M.Y.1    Kan, M.C.2    Lin-Chao, S.3
  • 8
    • 0030792287 scopus 로고    scopus 로고
    • New pc versions of the kinetic-simulation and fitting programs, KINSIM and FITSIM
    • Dang Q, Frieden C. 1997. New PC versions of the kinetic-simulation and fitting programs, KINSIM and FITSIM. Trends Biochem Sci 22:317.
    • (1997) Trends Biochem Sci , vol.22 , pp. 317
    • Dang, Q.1    Frieden, C.2
  • 10
    • 0004244993 scopus 로고
    • New York: Plenum Press
    • Diener TO, ed. 1987. The viroids. New York: Plenum Press.
    • (1987) The Viroids
    • Diener, T.O.1
  • 11
    • 0031260005 scopus 로고    scopus 로고
    • Cell-to-cell movement of potato spindle tuber viroid
    • Ding B, Kwon MO, Hammond R, Owens R. 1997. Cell-to-cell movement of potato spindle tuber viroid. Plant J 12:931-936.
    • (1997) Plant J , vol.12 , pp. 931-936
    • Ding, B.1    Kwon, M.O.2    Hammond, R.3    Owens, R.4
  • 13
    • 0031982168 scopus 로고    scopus 로고
    • A proposed scheme for viroid classification and nomenclature
    • Flores R, Randles JW, Bar-Joseph M, Diener TO. 1998. A proposed scheme for viroid classification and nomenclature. Arch Virol 143:623-629.
    • (1998) Arch Virol , vol.143 , pp. 623-629
    • Flores, R.1    Randles, J.W.2    Bar-Joseph, M.3    Diener, T.O.4
  • 14
    • 0016219032 scopus 로고
    • Characterization of T7-specific ribonucleic acid polymerase. IV. Resolution of the major in vitro transcripts by gel electrophoresis
    • Golomb M, Chamberlin M. 1974. Characterization of T7-specific ribonucleic acid polymerase. IV. Resolution of the major in vitro transcripts by gel electrophoresis. J Biol Chem 249:2858-2863.
    • (1974) J Biol Chem , vol.249 , pp. 2858-2863
    • Golomb, M.1    Chamberlin, M.2
  • 16
    • 0024832780 scopus 로고
    • Imaging of viroids in nuclei from tomato leaf tissue by in situ hybridization and confocal laser scanning microscopy
    • Harders J, Lukács N, Robert-Nicoud M, Jovin TM, Riesner D. 1989. Imaging of viroids in nuclei from tomato leaf tissue by in situ hybridization and confocal laser scanning microscopy. EMBO J 8:3941-3949.
    • (1989) EMBO J , vol.8 , pp. 3941-3949
    • Harders, J.1    Lukács, N.2    Robert-Nicoud, M.3    Jovin, T.M.4    Riesner, D.5
  • 17
    • 0024210057 scopus 로고
    • Analysis of RNA structure by temperature-gradient gel electrophoresis: Viroid replication and processing
    • Hecker R, Wang Z, Steger G, Riesner D. 1988. Analysis of RNA structure by temperature-gradient gel electrophoresis: Viroid replication and processing. Gene 72:59-74.
    • (1988) Gene , vol.72 , pp. 59-74
    • Hecker, R.1    Wang, Z.2    Steger, G.3    Riesner, D.4
  • 19
    • 0018788109 scopus 로고
    • Fine structure melting of viroids as studied by kinetic methods
    • Henco K, Sänger HL, Riesner D. 1979. Fine structure melting of viroids as studied by kinetic methods. Nucleic Acids Res 6:3041-3059.
    • (1979) Nucleic Acids Res , vol.6 , pp. 3041-3059
    • Henco, K.1    Sänger, H.L.2    Riesner, D.3
  • 20
    • 0020479047 scopus 로고
    • Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template
    • Kadesch TR, Chamberlin MJ. 1982. Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template. J Biol Chem 257:5286-5295.
    • (1982) J Biol Chem , vol.257 , pp. 5286-5295
    • Kadesch, T.R.1    Chamberlin, M.J.2
  • 21
    • 0345661218 scopus 로고    scopus 로고
    • For obtaining the program see
    • KinSim. 1998. For obtaining the program see: http://www.biochem. wustl.edu/cflab/, http://unix.hensa.ac.uk/cgi-bin/cftp/wuarchive. wustl.edu/packages/kinsim and ftp://wuarchive.wustl.edu/ packages/kinsim.
    • (1998)
  • 22
    • 0024418275 scopus 로고
    • A scheme for viroid classification
    • Koltunow AM, Rezaian MA. 1989. A scheme for viroid classification. Intervirology 30:194-201.
    • (1989) Intervirology , vol.30 , pp. 194-201
    • Koltunow, A.M.1    Rezaian, M.A.2
  • 23
    • 0027305857 scopus 로고
    • Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase
    • Lewicki BT, Margus T, Remme J, Nierhaus KH. 1993. Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase. J Mol Biol 231:581-593.
    • (1993) J Mol Biol , vol.231 , pp. 581-593
    • Lewicki, B.T.1    Margus, T.2    Remme, J.3    Nierhaus, K.H.4
  • 24
    • 0025981740 scopus 로고
    • Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA
    • Loss P, Schmitz M, Steger G, Riesner D. 1991. Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA. EMBO J 10:719-727.
    • (1991) EMBO J , vol.10 , pp. 719-727
    • Loss, P.1    Schmitz, M.2    Steger, G.3    Riesner, D.4
  • 25
    • 0002426872 scopus 로고
    • Transcription of eukaryotic genes in a whole-cell extract
    • Hames BD, Higgins SJ, eds. Oxford, UK, Washington, DC: IRL Press
    • Manley JL. 1984. Transcription of eukaryotic genes in a whole-cell extract. In: Hames BD, Higgins SJ, eds. Transcription and translation - a practical approach. Oxford, UK, Washington, DC: IRL Press, pp 71-88.
    • (1984) Transcription and Translation - A Practical Approach , pp. 71-88
    • Manley, J.L.1
  • 26
    • 0001931563 scopus 로고
    • Transcription of RNA in isolated nuclei
    • Hames BD, Higgins SJ, eds. Oxford, UK, Washington, DC: IRL Press
    • Marzluff WF, Huang RCC. 1984. Transcription of RNA in isolated nuclei. In: Hames BD, Higgins SJ, eds. Transcription and translation - a practical approach. Oxford, UK, Washington, DC: IRL Press, pp 89-129.
    • (1984) Transcription and Translation - A Practical Approach , pp. 89-129
    • Marzluff, W.F.1    Huang, R.C.C.2
  • 27
    • 0025341582 scopus 로고
    • A mechanism of formation of a persistent hybrid between elongating RNA and template DNA
    • Masukata H, Tomizawa J. 1990. A mechanism of formation of a persistent hybrid between elongating RNA and template DNA. Cell 62:331-338.
    • (1990) Cell , vol.62 , pp. 331-338
    • Masukata, H.1    Tomizawa, J.2
  • 28
    • 0018394988 scopus 로고
    • Viroid replication is inhibited by α-amanitin
    • Mühlbach HP, Sänger HL. 1979. Viroid replication is inhibited by α-amanitin. Nature 278:185-188.
    • (1979) Nature , vol.278 , pp. 185-188
    • Mühlbach, H.P.1    Sänger, H.L.2
  • 29
    • 0019779738 scopus 로고
    • Sequential folding of a messenger RNA molecule
    • Nussinov R, Tinoco I Jr. 1981. Sequential folding of a messenger RNA molecule. J Mol Biol 151:519-533.
    • (1981) J Mol Biol , vol.151 , pp. 519-533
    • Nussinov, R.1    Tinoco I., Jr.2
  • 30
    • 0027215283 scopus 로고
    • Multiple pathways of reversion in viroids for conservation of structural elements
    • Qu F, Heinrich C, Loss P, Steger G, Tien P, Riesner D. 1993. Multiple pathways of reversion in viroids for conservation of structural elements. EMBO J 12:2129-2139.
    • (1993) EMBO J , vol.12 , pp. 2129-2139
    • Qu, F.1    Heinrich, C.2    Loss, P.3    Steger, G.4    Tien, P.5    Riesner, D.6
  • 31
    • 0002262619 scopus 로고
    • Structure of viroids and their replication intermediates: Are thermodynamic domains also functional domains?
    • Riesner D. 1990. Structure of viroids and their replication intermediates: Are thermodynamic domains also functional domains? Sem Virol 1:83-99.
    • (1990) Sem Virol , vol.1 , pp. 83-99
    • Riesner, D.1
  • 33
    • 0001123611 scopus 로고
    • Temperature-gradient gel electrophoresis: A method for the analysis of conformational transitions and mutations in nucleic acids and proteins
    • Chrambach A, Dunn MJ, Radola BJ, ed. Weinheim, Germany: VCH Verlagsgesellschaft
    • Riesner D, Henco K, Steger G. 1991. Temperature-gradient gel electrophoresis: A method for the analysis of conformational transitions and mutations in nucleic acids and proteins. In: Chrambach A, Dunn MJ, Radola BJ, ed. Advances in electrophoresis. Vol. 4. Weinheim, Germany: VCH Verlagsgesellschaft, pp 169-250.
    • (1991) Advances in Electrophoresis , vol.4 , pp. 169-250
    • Riesner, D.1    Henco, K.2    Steger, G.3
  • 35
    • 0024314357 scopus 로고
    • Temperature-gradient gel electrophoresis: Analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions
    • Riesner D, Steger G, Zimmat R, Owens RA, Wagenhöfer M, Hillen W, Vollbach S, Henco K. 1989. Temperature-gradient gel electrophoresis: Analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions. Electrophoresis 10:377-389.
    • (1989) Electrophoresis , vol.10 , pp. 377-389
    • Riesner, D.1    Steger, G.2    Zimmat, R.3    Owens, R.A.4    Wagenhöfer, M.5    Hillen, W.6    Vollbach, S.7    Henco, K.8
  • 36
    • 0023180292 scopus 로고
    • Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts
    • Rosenbaum V, Riesner D. 1987. Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys Chem 26:235-246.
    • (1987) Biophys Chem , vol.26 , pp. 235-246
    • Rosenbaum, V.1    Riesner, D.2
  • 37
    • 0001668440 scopus 로고
    • Involvement of nuclear DNA-dependent RNA polymerases in potato spindle tuber viroid replication: A reevaluation
    • Schindler IM, Mühlbach HP. 1992. Involvement of nuclear DNA-dependent RNA polymerases in potato spindle tuber viroid replication: A reevaluation. Plant Sci 8:221-229.
    • (1992) Plant Sci , vol.8 , pp. 221-229
    • Schindler, I.M.1    Mühlbach, H.P.2
  • 38
    • 0021008593 scopus 로고
    • A two-dimensional electrophoretic technique for the detection of circular viroids and virusoids
    • Schumacher J, Randles JW, Riesner D. 1983. A two-dimensional electrophoretic technique for the detection of circular viroids and virusoids. Anal Biochem 135:288-295.
    • (1983) Anal Biochem , vol.135 , pp. 288-295
    • Schumacher, J.1    Randles, J.W.2    Riesner, D.3
  • 40
    • 0021532353 scopus 로고
    • Conformational transitions in viroids and virusoids: Comparison of results from energy minimization algorithm and from experimental data
    • Steger H, Hofmann G, Förtsch J, Gross HJ, Randles JW, Sänger HL, Riesner D. 1984. Conformational transitions in viroids and virusoids: Comparison of results from energy minimization algorithm and from experimental data. J Biomol Struct Dyn 2:543-571.
    • (1984) J Biomol Struct Dyn , vol.2 , pp. 543-571
    • Steger, H.1    Hofmann, G.2    Förtsch, J.3    Gross, H.J.4    Randles, J.W.5    Sänger, H.L.6    Riesner, D.7
  • 41
    • 0023055397 scopus 로고
    • Structure of viroid replicative intermediates: Physico-chemical studies on SP6 transcripts of cloned oligomeric potato spindle tuber viroid
    • Steger G, Tabler M, Brüggemann W, Colpan M, Klotz G, Sänger HL, Riesner D. 1986. Structure of viroid replicative intermediates: Physico-chemical studies on SP6 transcripts of cloned oligomeric potato spindle tuber viroid. Nucleic Acids Res 14:9613-9630.
    • (1986) Nucleic Acids Res , vol.14 , pp. 9613-9630
    • Steger, G.1    Tabler, M.2    Brüggemann, W.3    Colpan, M.4    Klotz, G.5    Sänger, H.L.6    Riesner, D.7
  • 42
    • 0023148539 scopus 로고
    • Oligomeric potato spindle tuber viroid RNA does not process autocatalytically under conditions where other RNAs do
    • Tsagris M, Tabler M, Sänger HL. 1987. Oligomeric potato spindle tuber viroid RNA does not process autocatalytically under conditions where other RNAs do. Virology 157:227-231.
    • (1987) Virology , vol.157 , pp. 227-231
    • Tsagris, M.1    Tabler, M.2    Sänger, H.L.3


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