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Volumn 3, Issue 1, 1997, Pages 1-16

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element

Author keywords

methylation; retrotransposon; reverse transcriptase; RNA folding

Indexed keywords

RNA; RNA DIRECTED DNA POLYMERASE;

EID: 0031014702     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (73)

References (64)
  • 1
    • 0027434244 scopus 로고
    • Thermal unfolding of a group I ribozyme: The low-temperature transition is primarily disruption of tertiary structure
    • Banerjee AR, Jaeger JA, Turner DH. 1993. Thermal unfolding of a group I ribozyme: The low-temperature transition is primarily disruption of tertiary structure. Biochemistry 32:153-163.
    • (1993) Biochemistry , vol.32 , pp. 153-163
    • Banerjee, A.R.1    Jaeger, J.A.2    Turner, D.H.3
  • 2
    • 0024025172 scopus 로고
    • Deletion of nonconserved helixes near the 3′ end of the rRNA intron of Tetrahymena thermophila alters selfsplicing but not core catalytic activity
    • Barfod ET, Cech TR. 1988. Deletion of nonconserved helixes near the 3′ end of the rRNA intron of Tetrahymena thermophila alters selfsplicing but not core catalytic activity. Genes & Dev 2:652-663.
    • (1988) Genes & Dev , vol.2 , pp. 652-663
    • Barfod, E.T.1    Cech, T.R.2
  • 4
    • 0023351699 scopus 로고
    • The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme
    • Burke WD, Catalang CC, Eickbush TH. 1987. The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme. Mol Cell Biol 7:2221-2230.
    • (1987) Mol Cell Biol , vol.7 , pp. 2221-2230
    • Burke, W.D.1    Catalang, C.C.2    Eickbush, T.H.3
  • 5
    • 0028871801 scopus 로고
    • R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes
    • Burke WD, Müller F, Eickbush TH. 1995. R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes. Nucleic Acids Res 23:4628-4634.
    • (1995) Nucleic Acids Res , vol.23 , pp. 4628-4634
    • Burke, W.D.1    Müller, F.2    Eickbush, T.H.3
  • 7
    • 0016169138 scopus 로고
    • The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA
    • Crothers DM, Cole PE, Hilbers CW, Shulman RG. 1974. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol Biol 87:63-88.
    • (1974) J. Mol Biol , vol.87 , pp. 63-88
    • Crothers, D.M.1    Cole, P.E.2    Hilbers, C.W.3    Shulman, R.G.4
  • 8
    • 0029904020 scopus 로고    scopus 로고
    • Solution structure of an ATP-binding RNA aptamer reveals a novel fold
    • Dieckmann T, Suzuki E, Feigon J, Nakamura GK. 1996. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA 2:628-640.
    • (1996) RNA , vol.2 , pp. 628-640
    • Dieckmann, T.1    Suzuki, E.2    Feigon, J.3    Nakamura, G.K.4
  • 10
    • 0028870386 scopus 로고
    • Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup
    • Eickbush DG, Eickbush TH. 1995. Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics 139:671-684.
    • (1995) Genetics , vol.139 , pp. 671-684
    • Eickbush, D.G.1    Eickbush, T.H.2
  • 11
    • 0028894297 scopus 로고
    • R1 and R2 retrotransposable elements of Drosophila evolve at rates similar to those of nuclear genes
    • Eickbush DG, Lathe WC III, Francino MP, Eickbush TH. 1995. R1 and R2 retrotransposable elements of Drosophila evolve at rates similar to those of nuclear genes. Genetics 139:685-695.
    • (1995) Genetics , vol.139 , pp. 685-695
    • Eickbush, D.G.1    Lathe III, W.C.2    Francino, M.P.3    Eickbush, T.H.4
  • 15
    • 0029382234 scopus 로고
    • G·U base pairing motifs in ribosomal RNA
    • Gautheret D, Konings D, Gutell RR. 1995. G·U base pairing motifs in ribosomal RNA. RNA 1:807-814.
    • (1995) RNA , vol.1 , pp. 807-814
    • Gautheret, D.1    Konings, D.2    Gutell, R.R.3
  • 16
    • 0029082074 scopus 로고
    • Determination of the folding topology of the S11 RNA from Caenorhabditis elegans by multidimensional heteronuclear NMR
    • Greenbaum NL, Radhakrishnan I, Hirsh D, Patel DJ. 1995. Determination of the folding topology of the S11 RNA from Caenorhabditis elegans by multidimensional heteronuclear NMR. J Mol Biol 252:314-327.
    • (1995) J Mol Biol , vol.252 , pp. 314-327
    • Greenbaum, N.L.1    Radhakrishnan, I.2    Hirsh, D.3    Patel, D.J.4
  • 18
    • 0026423027 scopus 로고
    • Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops
    • Heus HA, Pardi A. 1991. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253:191-194.
    • (1991) Science , vol.253 , pp. 191-194
    • Heus, H.A.1    Pardi, A.2
  • 20
    • 0026000848 scopus 로고
    • Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs
    • Holbrook SR, Cheong C, Tinoco I Jr, Kim S. 1991. Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 353:579-581.
    • (1991) Nature , vol.353 , pp. 579-581
    • Holbrook, S.R.1    Cheong, C.2    Tinoco Jr., I.3    Kim, S.4
  • 21
    • 0024284965 scopus 로고
    • A simple structural feature is a major determinant of the identity of transfer RNA
    • Hou YM, Schimmel P. 1988. A simple structural feature is a major determinant of the identity of transfer RNA. Nature 333:140-145.
    • (1988) Nature , vol.333 , pp. 140-145
    • Hou, Y.M.1    Schimmel, P.2
  • 22
    • 0021991295 scopus 로고
    • Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: A technique for RNA structure analysis using chemical probes and reverse transcriptase
    • Inoue T, Cech TR. 1985. Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: A technique for RNA structure analysis using chemical probes and reverse transcriptase. Proc Natl Acad Sci USA 82:648-652.
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 648-652
    • Inoue, T.1    Cech, T.R.2
  • 23
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • Jacobson H, Stockmayer WH. 1950. Intramolecular reaction in polycondensations. I. The theory of linear systems. J Chem Phys 18:1600-1606.
    • (1950) J Chem Phys , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 25
    • 0345005029 scopus 로고
    • Improved predictions of secondary structures for RNA
    • Jaeger JA, Turner DH, Zuker M. 1989. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA 86:7706-7710.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 7706-7710
    • Jaeger, J.A.1    Turner, D.H.2    Zuker, M.3
  • 26
    • 0025361553 scopus 로고
    • Predicting optimal and suboptimal secondary structure for RNA
    • Jaeger JA, Turner DH, Zuker M. 1990a. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol 183:281-306.
    • (1990) Methods Enzymol , vol.183 , pp. 281-306
    • Jaeger, J.A.1    Turner, D.H.2    Zuker, M.3
  • 28
    • 0027433710 scopus 로고
    • Monitoring of cooperative unfolding of the sunY group I intron of bacteriophage T4
    • Jaeger L, Westhof E, Michel F. 1993b. Monitoring of cooperative unfolding of the sunY group I intron of bacteriophage T4. J Mol Biol 234:331-346.
    • (1993) J Mol Biol , vol.234 , pp. 331-346
    • Jaeger, L.1    Westhof, E.2    Michel, F.3
  • 29
    • 0026322842 scopus 로고
    • Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects
    • Jakubczak JL, Burke WD, Eickbush TH. 1991. Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc Natl Acad Sci USA 88:3295-3299.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 3295-3299
    • Jakubczak, J.L.1    Burke, W.D.2    Eickbush, T.H.3
  • 30
    • 0025269132 scopus 로고
    • Type I (R1) and type II (R2) ribosomal DNA insertions of Drosophila melanogaster are retrotransposable elements closely related to those of Bombyx mori
    • Jakubczak JL, Xiong Y, Eickbush TH. 1990. Type I (R1) and type II (R2) ribosomal DNA insertions of Drosophila melanogaster are retrotransposable elements closely related to those of Bombyx mori. J Mol Biol 212:37-52.
    • (1990) J Mol Biol , vol.212 , pp. 37-52
    • Jakubczak, J.L.1    Xiong, Y.2    Eickbush, T.H.3
  • 31
    • 0024827733 scopus 로고
    • Phylogenetic comparative analysis of RNA secondary structure
    • James BD, Olsen GJ, Pace NR. 1989. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol 180:227-239.
    • (1989) Methods Enzymol , vol.180 , pp. 227-239
    • James, B.D.1    Olsen, G.J.2    Pace, N.R.3
  • 32
    • 0029946537 scopus 로고    scopus 로고
    • Structural basis or RNA folding and recognition in an AMP-RNA aptamer complex
    • Jiang F, Kumar RA, Jones RA, Patel DJ. 1996. Structural basis or RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382:183-186.
    • (1996) Nature , vol.382 , pp. 183-186
    • Jiang, F.1    Kumar, R.A.2    Jones, R.A.3    Patel, D.J.4
  • 33
    • 0028866812 scopus 로고
    • Solution structure of the CUUG hairpin loop: A novel RNA tetraloop motif
    • Jucker FM, Pardi A. 1995. Solution structure of the CUUG hairpin loop: A novel RNA tetraloop motif. Biochemistry 34:14416-14427.
    • (1995) Biochemistry , vol.34 , pp. 14416-14427
    • Jucker, F.M.1    Pardi, A.2
  • 35
    • 0029348884 scopus 로고
    • A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs
    • Konings DAM, Gutell RR. 1995. A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA 1:559-574.
    • (1995) RNA , vol.1 , pp. 559-574
    • Konings, D.A.M.1    Gutell, R.R.2
  • 36
    • 0024395268 scopus 로고
    • Pattern analysis of RNA secondary structure, similarity and consensus of minimal-energy folding
    • Konings DAM, Hogeweg P. 1989. Pattern analysis of RNA secondary structure, similarity and consensus of minimal-energy folding. J Mol Biol 207:597-614.
    • (1989) J Mol Biol , vol.207 , pp. 597-614
    • Konings, D.A.M.1    Hogeweg, P.2
  • 37
    • 0028234517 scopus 로고
    • Thermodynamics of RNA folding in a conserved ribosomal RNA domain
    • Laing LG, Draper J. 1994. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J Mol Biol 237:560-576.
    • (1994) J Mol Biol , vol.237 , pp. 560-576
    • Laing, L.G.1    Draper, J.2
  • 38
    • 0014561038 scopus 로고
    • Structural studies on transfer ribonucleic acid. I. Labeling of exposed guanine sites in yeast transfer ribonucleic acid with kethoxal
    • Litt M. 1969. Structural studies on transfer ribonucleic acid. I. Labeling of exposed guanine sites in yeast transfer ribonucleic acid with kethoxal. Biochemistry 8:3249-3253.
    • (1969) Biochemistry , vol.8 , pp. 3249-3253
    • Litt, M.1
  • 39
    • 0029058441 scopus 로고
    • RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element
    • Luan DD, Eickbush TH. 1995. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol 15:3882-3891.
    • (1995) Mol Cell Biol , vol.15 , pp. 3882-3891
    • Luan, D.D.1    Eickbush, T.H.2
  • 40
    • 0027450385 scopus 로고
    • Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition
    • Luan DD, Korman MH, Jakubczak JL, Eickbush TH. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition. Cell 72:595-605.
    • (1993) Cell , vol.72 , pp. 595-605
    • Luan, D.D.1    Korman, M.H.2    Jakubczak, J.L.3    Eickbush, T.H.4
  • 41
    • 0039161225 scopus 로고    scopus 로고
    • Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein
    • Luck R, Steger G, Riesner D. 1996. Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein. J Mol Biol 258:813-826.
    • (1996) J Mol Biol , vol.258 , pp. 813-826
    • Luck, R.1    Steger, G.2    Riesner, D.3
  • 42
    • 0024279871 scopus 로고
    • Changing the identity of a tRNA by introducing a G·U wobble pair near the 3′ acceptor end
    • McClain WH, Foss K. 1988. Changing the identity of a tRNA by introducing a G·U wobble pair near the 3′ acceptor end. Science 240:793-796.
    • (1988) Science , vol.240 , pp. 793-796
    • McClain, W.H.1    Foss, K.2
  • 43
    • 0025678737 scopus 로고
    • Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
    • Michel F, Westhof E. 1990. Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 216:585-610.
    • (1990) J Mol Biol , vol.216 , pp. 585-610
    • Michel, F.1    Westhof, E.2
  • 44
    • 0022470564 scopus 로고
    • Rapid chemical probing of conformation in 16S ribosomal RNA and 30S ribosomal subunits using primer extension
    • Moazed D, Stern S, Noller HF. 1986. Rapid chemical probing of conformation in 16S ribosomal RNA and 30S ribosomal subunits using primer extension. J Mol Biol 187:399-416.
    • (1986) J Mol Biol , vol.187 , pp. 399-416
    • Moazed, D.1    Stern, S.2    Noller, H.F.3
  • 46
    • 0028858599 scopus 로고
    • Solution structure of a bovine immunodeficiency virus TAT-Tar peptide-RNA complex
    • Puglisi JD, Chen L, Blanchard S, Frankel AD. 1995. Solution structure of a bovine immunodeficiency virus TAT-Tar peptide-RNA complex. Science 270:1200-1203.
    • (1995) Science , vol.270 , pp. 1200-1203
    • Puglisi, J.D.1    Chen, L.2    Blanchard, S.3    Frankel, A.D.4
  • 48
    • 0027146665 scopus 로고
    • 2 in solution from NMR and restrained molecular dynamics
    • 2 in solution from NMR and restrained molecular dynamics. Biochemistry 32:12612-12623.
    • (1993) Biochemistry , vol.32 , pp. 12612-12623
    • SantaLucia Jr., J.1    Turner, D.H.2
  • 49
    • 0026081968 scopus 로고
    • A rapid method for the purification of deprotected oligodeoxynucleotides
    • Sawadogo M, Van Dyke MW. 1991. A rapid method for the purification of deprotected oligodeoxynucleotides. Nucleic Acids Res 79:674.
    • (1991) Nucleic Acids Res , vol.79 , pp. 674
    • Sawadogo, M.1    Van Dyke, M.W.2
  • 50
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • Serra MJ, Turner DH. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol 259:242-261.
    • (1995) Methods Enzymol , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 51
    • 0028955347 scopus 로고
    • Minor groove recognition of the conserved G·U pair at the Tetrahymena ribozyme reaction site
    • Strobel SA, Cech TR. 1995. Minor groove recognition of the conserved G·U pair at the Tetrahymena ribozyme reaction site. Science 267:675-679.
    • (1995) Science , vol.267 , pp. 675-679
    • Strobel, S.A.1    Cech, T.R.2
  • 52
    • 0028953727 scopus 로고
    • The sarcin/ricin loop, a modular RNA
    • Szewczak AA, Moore PB. 1995. The sarcin/ricin loop, a modular RNA. J Mol Biol 247:81-98.
    • (1995) J Mol Biol , vol.247 , pp. 81-98
    • Szewczak, A.A.1    Moore, P.B.2
  • 54
    • 0025811124 scopus 로고
    • Structure of an unusually stable RNA hairpin
    • Varani G, Cheong C, Tinoco I Jr. 1991. Structure of an unusually stable RNA hairpin. Biochemistry 30:3280-3289.
    • (1991) Biochemistry , vol.30 , pp. 3280-3289
    • Varani, G.1    Cheong, C.2    Tinoco Jr., I.3
  • 55
    • 0026348081 scopus 로고
    • RNA structure and NMR spectroscopy
    • Varani G, Tinoco I Jr. 1991. RNA structure and NMR spectroscopy. Q Rev Biophys 24:479-532.
    • (1991) Q Rev Biophys , vol.24 , pp. 479-532
    • Varani, G.1    Tinoco Jr., I.2
  • 57
    • 0022551018 scopus 로고
    • Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA: Temperature factors and dynamics, coordinated waters, and base pair propeller twist angles
    • Westhof E, Sundaralingam M. 1986. Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA: Temperature factors and dynamics, coordinated waters, and base pair propeller twist angles. Biochemistry 25:4868-4878.
    • (1986) Biochemistry , vol.25 , pp. 4868-4878
    • Westhof, E.1    Sundaralingam, M.2
  • 58
    • 0024328777 scopus 로고
    • Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC
    • Williams AP, Longfellow CE, Freier SM, Kierzek R, Turner DH. 1989. Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry 28:4283-4291.
    • (1989) Biochemistry , vol.28 , pp. 4283-4291
    • Williams, A.P.1    Longfellow, C.E.2    Freier, S.M.3    Kierzek, R.4    Turner, D.H.5
  • 59
    • 0024293991 scopus 로고
    • Functional expression of a sequencespecific endonuclease encoded by the retrotransposon R2Bm
    • Xiong Y, Eickbush TH. 1988. Functional expression of a sequencespecific endonuclease encoded by the retrotransposon R2Bm. Cell 55:235-246.
    • (1988) Cell , vol.55 , pp. 235-246
    • Xiong, Y.1    Eickbush, T.H.2
  • 60
    • 0029972909 scopus 로고    scopus 로고
    • Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy
    • Yang Y, Kochogan M, Burgstaller P, Westhof E, Famulok M. 1996. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 272:1343-1347.
    • (1996) Science , vol.272 , pp. 1343-1347
    • Yang, Y.1    Kochogan, M.2    Burgstaller, P.3    Westhof, E.4    Famulok, M.5
  • 61
    • 0029613238 scopus 로고
    • Molecular recognition in the bovine immunodeficiency virus TAT peptide Tar RNA complex
    • Ye XM, Kumar RA, Patel DJ. 1995. Molecular recognition in the bovine immunodeficiency virus TAT peptide Tar RNA complex. Chem & Biol 2:827-840.
    • (1995) Chem & Biol , vol.2 , pp. 827-840
    • Ye, X.M.1    Kumar, R.A.2    Patel, D.J.3
  • 62
    • 0029312758 scopus 로고
    • Analysis of the structure of Tetrahymena nuclear RNAs in vivo: Telomerase RNA, the self-splicing rRNA intron, and U2 snRNA
    • Zaug AJ, Cech TR. 1995. Analysis of the structure of Tetrahymena nuclear RNAs in vivo: Telomerase RNA, the self-splicing rRNA intron, and U2 snRNA. RNA 1:363-374.
    • (1995) RNA , vol.1 , pp. 363-374
    • Zaug, A.J.1    Cech, T.R.2
  • 63
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 64
    • 0025731211 scopus 로고
    • A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison
    • Zuker M, Jaeger JA, Turner DH. 1991. A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res 19:2707-2714.
    • (1991) Nucleic Acids Res , vol.19 , pp. 2707-2714
    • Zuker, M.1    Jaeger, J.A.2    Turner, D.H.3


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