메뉴 건너뛰기




Volumn 10, Issue 2, 2004, Pages 176-184

The three-dimensional architecture of the class I ligase ribozyme

Author keywords

Molecular modeling; RNA catalysis; RNA structure

Indexed keywords

ADENOSINE TRIPHOSPHATE; HYDROXYL RADICAL; LIGASE; MAGNESIUM ION; PHOSPHORUS 32; RIBOZYME; RNA; RNA POLYMERASE;

EID: 1642499418     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5177504     Document Type: Article
Times cited : (38)

References (37)
  • 1
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
    • Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 2
    • 0002146655 scopus 로고    scopus 로고
    • Re-creating an RNA replicase
    • (eds. R.F. Gesteland et al.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Bartel, D.P. 1999. Re-creating an RNA replicase. In The RNA world, 2nd ed. (eds. R.F. Gesteland et al.), pp. 143-162. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1999) The RNA World, 2nd Ed. , pp. 143-162
    • Bartel, D.P.1
  • 3
    • 0034696587 scopus 로고    scopus 로고
    • Kinetic framework for ligation by an efficient RNA ligase ribozyme
    • Bergman, N.H., Johnston, W.K., and Bartel, D.P. 2000. Kinetic framework for ligation by an efficient RNA ligase ribozyme. Biochemistry 39: 3115-3123.
    • (2000) Biochemistry , vol.39 , pp. 3115-3123
    • Bergman, N.H.1    Johnston, W.K.2    Bartel, D.P.3
  • 5
    • 0025023607 scopus 로고
    • Iron (II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms
    • Celander, D.W. and Cech, T.R. 1990. Iron (II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms. Biochemistry 29: 1355-1361.
    • (1990) Biochemistry , vol.29 , pp. 1355-1361
    • Celander, D.W.1    Cech, T.R.2
  • 6
    • 0025963132 scopus 로고
    • Visualizing the higher order folding of a catalytic RNA molecule
    • -. 1991. Visualizing the higher order folding of a catalytic RNA molecule. Science 251: 401-407.
    • (1991) Science , vol.251 , pp. 401-407
  • 7
    • 0025071240 scopus 로고
    • Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC
    • Cheong, C., Varani, G., and Tinoco Jr., I. 1990. Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature 346: 680-682.
    • (1990) Nature , vol.346 , pp. 680-682
    • Cheong, C.1    Varani, G.2    Tinoco Jr., I.3
  • 8
    • 0033613230 scopus 로고    scopus 로고
    • The track of the pre-tRNA 5′ leader in the ribonuclease P ribozyme-substrate complex
    • Christian, E.L. and Harris, M.E. 1999. The track of the pre-tRNA 5′ leader in the ribonuclease P ribozyme-substrate complex. Biochemistry 38: 12629-12638.
    • (1999) Biochemistry , vol.38 , pp. 12629-12638
    • Christian, E.L.1    Harris, M.E.2
  • 10
    • 0021891882 scopus 로고
    • Nucleoside phosphorothioates
    • Eckstein, F. 1985. Nucleoside phosphorothioates. Annu. Rev. Biochem. 54: 367-402.
    • (1985) Annu. Rev. Biochem. , vol.54 , pp. 367-402
    • Eckstein, F.1
  • 11
    • 0029093855 scopus 로고
    • The secondary structure and sequence optimization of an RNA ligase ribozyme
    • Ekland, E.H. and Bartel, D.P. 1995. The secondary structure and sequence optimization of an RNA ligase ribozyme. Nucleic Acids Res. 23: 3231-3238.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 3231-3238
    • Ekland, E.H.1    Bartel, D.P.2
  • 12
    • 0029832218 scopus 로고    scopus 로고
    • RNA-catalysed RNA polymerization using nucleoside triphosphates
    • -. 1996. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 382: 373-376.
    • (1996) Nature , vol.382 , pp. 373-376
  • 13
    • 0029147392 scopus 로고
    • Structurally complex and highly active RNA ligases derived from random RNA sequences
    • Ekland, E.H., Szostak, J.W., and Bartel, D.P. 1995. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269: 364-370.
    • (1995) Science , vol.269 , pp. 364-370
    • Ekland, E.H.1    Szostak, J.W.2    Bartel, D.P.3
  • 14
    • 0032005336 scopus 로고    scopus 로고
    • Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions
    • Favre, A., Saintome, C., Fourrey, J.L., Clivio, P., and Laugaa, P. 1998. Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions. J. Photochem. Photobiol. B 42: 109-124.
    • (1998) J. Photochem. Photobiol. B , vol.42 , pp. 109-124
    • Favre, A.1    Saintome, C.2    Fourrey, J.L.3    Clivio, P.4    Laugaa, P.5
  • 15
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare, A.R., Zhou, K., and Doudna, J.A. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre-D'Amare, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 16
    • 0034687717 scopus 로고    scopus 로고
    • Recognition of nucleoside triphosphates during RNA-catalyzed primer extension
    • Glasner, M.E., Yen, C.C., Ekland, E.H., and Bartel, D.P. 2000. Recognition of nucleoside triphosphates during RNA-catalyzed primer extension. Biochemistry 39: 15556-15562.
    • (2000) Biochemistry , vol.39 , pp. 15556-15562
    • Glasner, M.E.1    Yen, C.C.2    Ekland, E.H.3    Bartel, D.P.4
  • 17
    • 0037172779 scopus 로고    scopus 로고
    • Metal ion requirements for structure and catalysis of an RNA ligase ribozyme
    • Glasner, M.E., Bergman, N.H., and Bartel, D.P. 2002. Metal ion requirements for structure and catalysis of an RNA ligase ribozyme. Biochemistry 41: 8103-8112.
    • (2002) Biochemistry , vol.41 , pp. 8103-8112
    • Glasner, M.E.1    Bergman, N.H.2    Bartel, D.P.3
  • 18
    • 0021762388 scopus 로고
    • Cleavage of DNA with methidiumpropyl-EDTA-iron(II): Reaction conditions and product analyses
    • Hertzberg, R.P. and Dervan, P.B. 1984. Cleavage of DNA with methidiumpropyl-EDTA-iron(II): Reaction conditions and product analyses. Biochemistry 23: 3934-3945.
    • (1984) Biochemistry , vol.23 , pp. 3934-3945
    • Hertzberg, R.P.1    Dervan, P.B.2
  • 19
    • 0035906978 scopus 로고    scopus 로고
    • RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension
    • Johnston, W.K., Unrau, P.J., Lawrence, M.S., Glasner, M.E., and Bartel, D.P. 2001. RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension. Science 292: 1319-1325.
    • (2001) Science , vol.292 , pp. 1319-1325
    • Johnston, W.K.1    Unrau, P.J.2    Lawrence, M.S.3    Glasner, M.E.4    Bartel, D.P.5
  • 20
    • 0033655139 scopus 로고    scopus 로고
    • Directed hydroxyl radical probing using iron(II) tethered to RNA
    • Joseph, S. and Noller, H.F. 2000. Directed hydroxyl radical probing using iron(II) tethered to RNA. Methods Enzymol. 318: 175-190.
    • (2000) Methods Enzymol. , vol.318 , pp. 175-190
    • Joseph, S.1    Noller, H.F.2
  • 21
    • 0002622819 scopus 로고    scopus 로고
    • Prospects for understanding the origin of the RNA world
    • (eds. R.F. Gesteland et al.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Joyce, G.F. and Orgel, L.E. 1999. Prospects for understanding the origin of the RNA world. In The RNA world, 2nd ed. (eds. R.F. Gesteland et al.), pp. 49-77. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1999) The RNA World, 2nd Ed. , pp. 49-77
    • Joyce, G.F.1    Orgel, L.E.2
  • 22
    • 0032827799 scopus 로고    scopus 로고
    • A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase
    • Kao, C., Zheng, M., and Rudisser, S. 1999. A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase. RNA 5: 1268-1272.
    • (1999) RNA , vol.5 , pp. 1268-1272
    • Kao, C.1    Zheng, M.2    Rudisser, S.3
  • 24
    • 0024359787 scopus 로고
    • Defining the inside and outside of a catalytic RNA molecule
    • Latham, J.A. and Cech, T.R. 1989. Defining the inside and outside of a catalytic RNA molecule. Science 245: 276-282.
    • (1989) Science , vol.245 , pp. 276-282
    • Latham, J.A.1    Cech, T.R.2
  • 25
    • 0032232529 scopus 로고    scopus 로고
    • MANIP: An interactive tool for modelling RNA
    • Massire, C. and Westhof, E. 1998. MANIP: An interactive tool for modelling RNA. J. Mol. Graph. Model 16: 197-205, 255-257.
    • (1998) J. Mol. Graph. Model , vol.16 , pp. 197-205
    • Massire, C.1    Westhof, E.2
  • 26
    • 0028500393 scopus 로고
    • DRAWNA: A program for drawing schematic views of nucleic acids
    • Massire, C., Gaspin, C., and Westhof, E. 1994. DRAWNA: A program for drawing schematic views of nucleic acids. J. Mol. Graph 12: 201-206.
    • (1994) J. Mol. Graph , vol.12 , pp. 201-206
    • Massire, C.1    Gaspin, C.2    Westhof, E.3
  • 27
    • 0026680843 scopus 로고
    • Site-specific modification of pre-mRNA: The 2′-hydroxyl groups at the splice sites
    • Moore, M.J. and Sharp, P.A. 1992. Site-specific modification of pre-mRNA: The 2′-hydroxyl groups at the splice sites. Science 256: 992-997.
    • (1992) Science , vol.256 , pp. 992-997
    • Moore, M.J.1    Sharp, P.A.2
  • 28
    • 0028945859 scopus 로고
    • Higher Order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P
    • Pan, T. 1995. Higher Order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 34: 902-909.
    • (1995) Biochemistry , vol.34 , pp. 902-909
    • Pan, T.1
  • 29
    • 0030669671 scopus 로고    scopus 로고
    • Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity
    • Pan, T. and Sosnick, T.R. 1997. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. Nat. Struct. Biol. 4: 931-938.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 931-938
    • Pan, T.1    Sosnick, T.R.2
  • 30
    • 0033520410 scopus 로고    scopus 로고
    • New pathways in folding of the Tetrahymena group I RNA enzyme
    • Russell, R. and Herschlag, D. 1999. New pathways in folding of the Tetrahymena group I RNA enzyme. J. Mol. Biol. 291: 1155-1167.
    • (1999) J. Mol. Biol. , vol.291 , pp. 1155-1167
    • Russell, R.1    Herschlag, D.2
  • 31
    • 0033485559 scopus 로고    scopus 로고
    • Non-unity molecular heritability demonstrated by continuous evolution in vitro
    • Schmitt, T. and Lehman, N. 1999. Non-unity molecular heritability demonstrated by continuous evolution in vitro. Chemis. Biol. 6: 857-869.
    • (1999) Chemis. Biol. , vol.6 , pp. 857-869
    • Schmitt, T.1    Lehman, N.2
  • 32
    • 0032319210 scopus 로고    scopus 로고
    • Following the folding of RNA with time-resolved synchrotron X-ray footprinting
    • Sclavi, B., Woodson, S., Sullivan, M., Chance, M., and Brenowitz, M. 1998. Following the folding of RNA with time-resolved synchrotron X-ray footprinting. Methods Enzymol. 295: 379-402.
    • (1998) Methods Enzymol. , vol.295 , pp. 379-402
    • Sclavi, B.1    Woodson, S.2    Sullivan, M.3    Chance, M.4    Brenowitz, M.5
  • 33
    • 0027739853 scopus 로고
    • The U5 and U6 small nuclear RNAs as active site components of the spliceosome
    • Sontheimer, E.J. and Steitz, J.A. 1993. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262: 1989-1996.
    • (1993) Science , vol.262 , pp. 1989-1996
    • Sontheimer, E.J.1    Steitz, J.A.2
  • 34
    • 0001268975 scopus 로고
    • Hydroxyl radical "footprinting": High-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein
    • Tullius, T.D. and Dombroski, B.A. 1986. Hydroxyl radical "footprinting": High-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein. Proc. Natl. Acad. Sci. 83: 5469-5473.
    • (1986) Proc. Natl. Acad. Sci. , vol.83 , pp. 5469-5473
    • Tullius, T.D.1    Dombroski, B.A.2
  • 35
    • 0023623752 scopus 로고
    • Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts
    • Tullius, T.D., Dombroski, B.A., Churchill, M.E., and Kam, L. 1987. Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts. Methods Enzymol. 155: 537-558.
    • (1987) Methods Enzymol. , vol.155 , pp. 537-558
    • Tullius, T.D.1    Dombroski, B.A.2    Churchill, M.E.3    Kam, L.4
  • 36
    • 0001320146 scopus 로고
    • Modeling the three-dimensional structure of ribonucleic acids
    • Westhof, E. 1993. Modeling the three-dimensional structure of ribonucleic acids. J. Mol. Struct. 286: 203-210.
    • (1993) J. Mol. Struct. , vol.286 , pp. 203-210
    • Westhof, E.1
  • 37
    • 0020587399 scopus 로고
    • The mechanism of free base formation from DNA by bleomycin. A proposal based on site specific tritium release from Poly(dA.dU)
    • Wu, J.C., Kozarich, J.W., and Stubbe, J. 1983. The mechanism of free base formation from DNA by bleomycin. A proposal based on site specific tritium release from Poly(dA.dU). J. Biol. Chem. 258: 4694-4697.
    • (1983) J. Biol. Chem. , vol.258 , pp. 4694-4697
    • Wu, J.C.1    Kozarich, J.W.2    Stubbe, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.