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Volumn 291, Issue 2, 1999, Pages 283-294

Sequential folding of the genomic ribozyme of the hepatitis delta virus: Structural analysis of RNA transcription intermediates

Author keywords

HDV; Hepatitis delta virus; Ribozyme; RNA folding; RNA structure probing

Indexed keywords

DIVALENT CATION; LEAD; OLIGORIBONUCLEOTIDE; RIBOZYME;

EID: 0032804538     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2955     Document Type: Article
Times cited : (35)

References (45)
  • 1
    • 0030803589 scopus 로고    scopus 로고
    • The self cleaving ribozymes of hepatitis delta virus
    • Been M. D., Wickham G. S. The self cleaving ribozymes of hepatitis delta virus. Eur. J. Biochem. 247:1997;741-753.
    • (1997) Eur. J. Biochem. , vol.247 , pp. 741-753
    • Been, M.D.1    Wickham, G.S.2
  • 5
    • 0022433369 scopus 로고
    • Crystallographic and biochemical investigation of the lead (II)-catalyzed hydrolysis of yeast phenylalanine tRNA
    • Brown R. S., Dewan J. C., Klug A. Crystallographic and biochemical investigation of the lead (II)-catalyzed hydrolysis of yeast phenylalanine tRNA. Biochemistry. 24:1985;4785-4801.
    • (1985) Biochemistry , vol.24 , pp. 4785-4801
    • Brown, R.S.1    Dewan, J.C.2    Klug, A.3
  • 6
    • 0025771080 scopus 로고
    • Three-dimensional model of Escherichia coli ribosomal 5S RNA as deduced from structure probing in solution and computer modeling
    • Brunel C. H., Romby P., Westhof E., Ehresmann C., Ehresmann B. Three-dimensional model of Escherichia coli ribosomal 5S RNA as deduced from structure probing in solution and computer modeling. J. Mol. Biol. 221:1991;293-308.
    • (1991) J. Mol. Biol. , vol.221 , pp. 293-308
    • Brunel, C.H.1    Romby, P.2    Westhof, E.3    Ehresmann, C.4    Ehresmann, B.5
  • 9
    • 0026593382 scopus 로고
    • Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA-ribosomal-protein complexes by means of Pb(II)-induced hydrolysis
    • Ciesiolka J., Lorenz S., Erdmann V. A. Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA-ribosomal-protein complexes by means of Pb(II)-induced hydrolysis. Eur. J. Biochem. 204, 1992a;575-581.
    • (1992) Eur. J. Biochem. , vol.204 , pp. 575-581
    • Ciesiolka, J.1    Lorenz, S.2    Erdmann, V.A.3
  • 10
    • 0026580484 scopus 로고
    • Different conformational forms of Escherichia coli and rat liver 5S rRNA revealed by Pb(II)-induced hydrolysis
    • Ciesiolka J., Lorenz S., Erdmann V. A. Different conformational forms of Escherichia coli and rat liver 5S rRNA revealed by Pb(II)-induced hydrolysis. Eur. J. Biochem. 204:1992b;583-589.
    • (1992) Eur. J. Biochem. , vol.204 , pp. 583-589
    • Ciesiolka, J.1    Lorenz, S.2    Erdmann, V.A.3
  • 14
    • 0029880537 scopus 로고    scopus 로고
    • Strategies for RNA folding
    • Draper D. E. Strategies for RNA folding. Trends Biochem. Sci. 21:1996b;145-149.
    • (1996) Trends Biochem. Sci. , vol.21 , pp. 145-149
    • Draper, D.E.1
  • 15
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare A. R., Zhou K., Doudna J. A. Crystal structure of a hepatitis delta virus ribozyme. Nature. 395:1998;567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre-D'Amare, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 17
    • 0027932176 scopus 로고
    • Thermodynamics of folding a pseudoknotted mRNA fragment
    • Gluick T. C., Draper D. E. Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241:1994;246-262.
    • (1994) J. Mol. Biol. , vol.241 , pp. 246-262
    • Gluick, T.C.1    Draper, D.E.2
  • 18
    • 0024564403 scopus 로고
    • Use of lead (II) to probe the structure of large RNA's. Conformation of the 3′ terminal domain of E. coli 16S rRNA and its involvement in building the tRNA binding sites
    • Górnicki P., Baudin F., Romby P., Wiewiórowski M., Krzyzosiak W. J., Ebel J. P., Ehresmann C. H., Ehresmann B. Use of lead (II) to probe the structure of large RNA's. Conformation of the 3′ terminal domain of E. coli 16S rRNA and its involvement in building the tRNA binding sites. J. Biomol. Struct. Dynam. 6:1989;971-984.
    • (1989) J. Biomol. Struct. Dynam. , vol.6 , pp. 971-984
    • Górnicki, P.1    Baudin, F.2    Romby, P.3    Wiewiórowski, M.4    Krzyzosiak, W.J.5    Ebel, J.P.6    Ehresmann, C.H.7    Ehresmann, B.8
  • 19
    • 0029061125 scopus 로고
    • The computer simulation of RNA folding pathways using a genetic algorithm
    • Gultyaev A. P., Van Batenburg F. H. D., Pleij C. W. A. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:1995;37-51.
    • (1995) J. Mol. Biol. , vol.250 , pp. 37-51
    • Gultyaev, A.P.1    Van Batenburg, F.H.D.2    Pleij, C.W.A.3
  • 21
    • 0025361553 scopus 로고
    • Predicting optimal and suboptimal secondary structure for RNA
    • Jaeger J. A., Turner D. H., Zuker M. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183:1990;281-306.
    • (1990) Methods Enzymol. , vol.183 , pp. 281-306
    • Jaeger, J.A.1    Turner, D.H.2    Zuker, M.3
  • 22
    • 0019837857 scopus 로고
    • Secondary structure formation during RNA synthesis
    • Kramer F. R., Mills D. R. Secondary structure formation during RNA synthesis. Nucleic Acids Res. 9:1981;5109-5124.
    • (1981) Nucleic Acids Res , vol.9 , pp. 5109-5124
    • Kramer, F.R.1    Mills, D.R.2
  • 23
    • 0024828055 scopus 로고
    • A guide for probing native small nuclear RNA and ribonucleoprotein structures
    • Krol A., Carbon P. A guide for probing native small nuclear RNA and ribonucleoprotein structures. Methods Enzymol. 180:1989;212-226.
    • (1989) Methods Enzymol. , vol.180 , pp. 212-226
    • Krol, A.1    Carbon, P.2
  • 25
    • 0027979491 scopus 로고
    • Chemical probing studies of variants of the genomic hepatitis delta virus ribozyme by primer extension analysis
    • Kumar P. K. R., Taira K., Nishikawa S. Chemical probing studies of variants of the genomic hepatitis delta virus ribozyme by primer extension analysis. Biochemistry. 33:1994;583-592.
    • (1994) Biochemistry , vol.33 , pp. 583-592
    • Kumar, P.K.R.1    Taira, K.2    Nishikawa, S.3
  • 26
    • 0029071510 scopus 로고
    • The molecular biology of hepatitis delta virus
    • Lai M. M. C. The molecular biology of hepatitis delta virus. Annu. Rev. Biochem. 64:1995;259-286.
    • (1995) Annu. Rev. Biochem. , vol.64 , pp. 259-286
    • Lai, M.M.C.1
  • 27
    • 0029295386 scopus 로고
    • Regulation of the hepatitis delta virus ribozymes: To cleave or not cleave?
    • Lazinski D. W., Taylor J. M. Regulation of the hepatitis delta virus ribozymes: to cleave or not cleave? RNA. 1:1995;225-233.
    • (1995) RNA , vol.1 , pp. 225-233
    • Lazinski, D.W.1    Taylor, J.M.2
  • 29
    • 0025597973 scopus 로고
    • The self-cleaving domain from the genomic RNA of hepatitis delta virus: Sequence requirements and the effects of denaturant
    • Perrotta A. T., Been M. D. The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant. Nucl. Acids Res. 18:1990;6821-6827.
    • (1990) Nucl. Acids Res. , vol.18 , pp. 6821-6827
    • Perrotta, A.T.1    Been, M.D.2
  • 30
    • 0025882069 scopus 로고
    • A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA
    • Perrotta A. T., Been M. D. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature. 350:1991;434-436.
    • (1991) Nature , vol.350 , pp. 434-436
    • Perrotta, A.T.1    Been, M.D.2
  • 31
    • 0032486091 scopus 로고    scopus 로고
    • A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation
    • Perrota A. T., Been M. D. A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation. J. Mol. Biol. 279:1998;361-373.
    • (1998) J. Mol. Biol. , vol.279 , pp. 361-373
    • Perrota, A.T.1    Been, M.D.2
  • 32
    • 0343799864 scopus 로고    scopus 로고
    • Inhibition of the self-cleavage reaction of the human hepatitis delta virus ribozyme by antibiotics
    • Rogers J., Chang A. H., Uwe von Ahsen ?., Schroeder R., Davies J. Inhibition of the self-cleavage reaction of the human hepatitis delta virus ribozyme by antibiotics. J. Mol. Biol. 259:1996;916-925.
    • (1996) J. Mol. Biol. , vol.259 , pp. 916-925
    • Rogers, J.1    Chang, A.H.2    Uwe Von Ahsen3    Schroeder, R.4    Davies, J.5
  • 33
    • 0026095948 scopus 로고
    • Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures
    • Rosenstein S. P., Been M. D. Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures. Nucl. Acids Res. 19:1991;5409-5416.
    • (1991) Nucl. Acids Res. , vol.19 , pp. 5409-5416
    • Rosenstein, S.P.1    Been, M.D.2
  • 34
    • 0020962741 scopus 로고
    • Lead ion binding and RNA chain hydrolysis in phenylalanine tRNA
    • Rubin J. R., Sundaralingam M. Lead ion binding and RNA chain hydrolysis in phenylalanine tRNA. J. Biomol. Struct. Dynam. 1:1983;639-646.
    • (1983) J. Biomol. Struct. Dynam. , vol.1 , pp. 639-646
    • Rubin, J.R.1    Sundaralingam, M.2
  • 36
    • 0029975949 scopus 로고    scopus 로고
    • Description of RNA folding by "simulated annealing"
    • Schmitz M., Steger G. Description of RNA folding by "Simulated annealing" J. Mol. Biol. 255:1996;254-266.
    • (1996) J. Mol. Biol. , vol.255 , pp. 254-266
    • Schmitz, M.1    Steger, G.2
  • 37
    • 0027305803 scopus 로고
    • Self-cleavage activity of the genomic HDV ribozyme in the presence of various divalent metal ions
    • Suh Y-A., Kumar P. K. R., Taira K., Nishikawa S. Self-cleavage activity of the genomic HDV ribozyme in the presence of various divalent metal ions. Nucl. Acids Res. 21:1993;3277-3280.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 3277-3280
    • Suh, Y.-A.1    Kumar, P.K.R.2    Taira, K.3    Nishikawa, S.4
  • 38
    • 0005784924 scopus 로고    scopus 로고
    • Hepatitis delta virus and its replication
    • B. N. Fields, D. M. Knipe, Howley P. M. et al. Philadelphia: Lippincott-Raven
    • Taylor J. M. Hepatitis delta virus and its replication. Fields B. N., Knipe D. M., Howley P. M. et al. Fields Virology. 1996;Lippincott-Raven, Philadelphia.
    • (1996) Fields Virology
    • Taylor, J.M.1
  • 39
    • 0001103473 scopus 로고    scopus 로고
    • Kinetics of folding of proteins and RNA
    • Thirumalai D., Woodson S. A. Kinetics of folding of proteins and RNA. Acc. Chem. Res. 29:1996;433-439.
    • (1996) Acc. Chem. Res. , vol.29 , pp. 433-439
    • Thirumalai, D.1    Woodson, S.A.2
  • 40
    • 0028143014 scopus 로고
    • Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
    • Walter A. E., Turner D. H. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry. 33:1994;12715-12719.
    • (1994) Biochemistry , vol.33 , pp. 12715-12719
    • Walter, A.E.1    Turner, D.H.2
  • 41
  • 44
    • 0032578472 scopus 로고    scopus 로고
    • RNA folding causes secondary structure rearrangement
    • Wu M., Tinoco I. Jr. RNA folding causes secondary structure rearrangement. Proc. Natl Acad. Sci. USA. 95:1998;11555-11560.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11555-11560
    • Wu, M.1    Tinoco I., Jr.2
  • 45
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zucker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zucker, M.1


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