메뉴 건너뛰기




Volumn 323, Issue 1, 2002, Pages 23-34

Functional group requirements in the probable active site of the VS ribozyme

Author keywords

2 aminopurine fluorescence; Acid base catalysis; Functional group modification; RNA catalysis

Indexed keywords

2 AMINOPURINE; ADENINE; AMINE; BASE; FUNCTIONAL GROUP; HYDROXYL GROUP; IMIDAZOLE; NUCLEIC ACID BASE; RIBOSE; RIBOZYME;

EID: 0036396544     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00910-5     Document Type: Article
Times cited : (58)

References (41)
  • 1
    • 0019856947 scopus 로고
    • In vitro splicing of the ribosomal RNA precursor of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence
    • Cech, T. R., Zaug, A. J. & Grabowski, P. J. (1981). In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell, 27, 487-496.
    • (1981) Cell , vol.27 , pp. 487-496
    • Cech, T.R.1    Zaug, A.J.2    Grabowski, P.J.3
  • 2
    • 0021013526 scopus 로고
    • The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
    • Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35, 849-857.
    • (1983) Cell , vol.35 , pp. 849-857
    • Guerrier-Takada, C.1    Gardiner, K.2    Marsh, T.3    Pace, N.4    Altman, S.5
  • 4
    • 0022446227 scopus 로고
    • Self-splicing of group II introns in vitro: Mapping of the branch point and mutational inhibition of lariat formation
    • Schmelzer, C. & Schweyen, R. J. (1986). Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation. Cell, 46, 557-565.
    • (1986) Cell , vol.46 , pp. 557-565
    • Schmelzer, C.1    Schweyen, R.J.2
  • 5
    • 0023663396 scopus 로고
    • Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
    • Forster, A. C. & Symons, R. H. (1987). Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell, 49, 211-220.
    • (1987) Cell , vol.49 , pp. 211-220
    • Forster, A.C.1    Symons, R.H.2
  • 6
    • 0023652361 scopus 로고
    • Self-cleaving transcripts of satellite DNA from the newt
    • Epstein, L. M. & Gall, J. G. (1987). Self-cleaving transcripts of satellite DNA from the newt. Cell, 48, 535-543.
    • (1987) Cell , vol.48 , pp. 535-543
    • Epstein, L.M.1    Gall, J.G.2
  • 7
    • 0022504693 scopus 로고
    • Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA
    • Buzayan, J. M., Gerlach, W. L. & Bruening, G. (1986). Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature, 323, 349-353.
    • (1986) Nature , vol.323 , pp. 349-353
    • Buzayan, J.M.1    Gerlach, W.L.2    Bruening, G.3
  • 8
    • 0023747377 scopus 로고
    • Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage
    • Sharmeen, L., Kuo, M. Y., Dinter-Gottlieb, G. & Taylor, J. (1988). Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J. Virol. 62, 2674-2679.
    • (1988) J. Virol. , vol.62 , pp. 2674-2679
    • Sharmeen, L.1    Kuo, M.Y.2    Dinter-Gottlieb, G.3    Taylor, J.4
  • 9
    • 0025333084 scopus 로고
    • A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria
    • Saville, B. J. & Collins, R. A. (1990). A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell, 61, 685-696.
    • (1990) Cell , vol.61 , pp. 685-696
    • Saville, B.J.1    Collins, R.A.2
  • 10
    • 0034637161 scopus 로고    scopus 로고
    • The structural basis of ribosome activity in peptide bond synthesis
    • Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.
    • (2000) Science , vol.289 , pp. 920-930
    • Nissen, P.1    Hansen, J.2    Ban, N.3    Moore, P.B.4    Steitz, T.A.5
  • 11
    • 0033965261 scopus 로고    scopus 로고
    • Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: Extending the parallels between the spliceosome and group II introns
    • Gordon, P. M., Sontheimer, E. J. & Piccirilli, J. A. (2000). Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: extending the parallels between the spliceosome and group II introns. RNA, 6, 199-205.
    • (2000) RNA , vol.6 , pp. 199-205
    • Gordon, P.M.1    Sontheimer, E.J.2    Piccirilli, J.A.3
  • 12
    • 0034649666 scopus 로고    scopus 로고
    • Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome
    • Yean, S.-L., Wuenschell, G., Termini, J. & Lin, R.-J. (2000). Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome. Nature, 408, 881-884.
    • (2000) Nature , vol.408 , pp. 881-884
    • Yean, S.-L.1    Wuenschell, G.2    Termini, J.3    Lin, R.-J.4
  • 13
    • 0035909314 scopus 로고    scopus 로고
    • Splicing-related catalysis by protein-free snRNAs
    • Valadkhan, S. & Manley, J. L. (2001). Splicing-related catalysis by protein-free snRNAs. Nature, 413, 701-707.
    • (2001) Nature , vol.413 , pp. 701-707
    • Valadkhan, S.1    Manley, J.L.2
  • 14
    • 0033150677 scopus 로고    scopus 로고
    • Structure, folding and catalysis in the small nucleolytic ribozymes
    • Lilley, D. M. J. (1999). Structure, folding and catalysis in the small nucleolytic ribozymes. Curr. Opin. Struct. Biol. 9, 330-338.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 330-338
    • Lilley, D.M.J.1
  • 16
    • 0035869008 scopus 로고    scopus 로고
    • Structure, folding and activity of the VS ribozyme: Importance of the 2-3-6 helical junction
    • Lafontaine, D. A., Norman, D. G. & Lilley, D. M. J. (2001). Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction. EMBO J. 20, 1415-1424.
    • (2001) EMBO J. , vol.20 , pp. 1415-1424
    • Lafontaine, D.A.1    Norman, D.G.2    Lilley, D.M.J.3
  • 17
    • 0037093486 scopus 로고    scopus 로고
    • The global structure of the VS ribozyme
    • Lafontaine, D. A., Norman, D. G. & Lilley, D. M. J. (2002). The global structure of the VS ribozyme. EMBO J. 21, 2461-2471.
    • (2002) EMBO J. , vol.21 , pp. 2461-2471
    • Lafontaine, D.A.1    Norman, D.G.2    Lilley, D.M.J.3
  • 18
    • 0029948820 scopus 로고    scopus 로고
    • A long-range pseudoknot is required for activity of the Neurospora VS ribozyme
    • Rastogi, T., Beattie, T. L., Olive, J. E. & Collins, R. A. (1996). A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. EMBO J. 15, 2820-2825.
    • (1996) EMBO J. , vol.15 , pp. 2820-2825
    • Rastogi, T.1    Beattie, T.L.2    Olive, J.E.3    Collins, R.A.4
  • 19
    • 0035965132 scopus 로고    scopus 로고
    • The A730 loop is an important component of the active site of the VS ribozyme
    • Lafontaine, D. A., Wilson, T. J., Norman, D. G. & Lilley, D. M. J. (2001). The A730 loop is an important component of the active site of the VS ribozyme. J. Mol. Biol. 312, 663-674.
    • (2001) J. Mol. Biol. , vol.312 , pp. 663-674
    • Lafontaine, D.A.1    Wilson, T.J.2    Norman, D.G.3    Lilley, D.M.J.4
  • 20
    • 0031564663 scopus 로고    scopus 로고
    • Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection
    • Beattie, T. L. & Collins, R. A. (1997). Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection. J. Mol. Biol. 267, 830-840.
    • (1997) J. Mol. Biol. , vol.267 , pp. 830-840
    • Beattie, T.L.1    Collins, R.A.2
  • 21
    • 0032475835 scopus 로고    scopus 로고
    • Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme
    • Sood, V. D., Beattie, T. L. & Collins, R. A. (1998). Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme. J. Mol. Biol. 282, 741-750.
    • (1998) J. Mol. Biol. , vol.282 , pp. 741-750
    • Sood, V.D.1    Beattie, T.L.2    Collins, R.A.3
  • 22
    • 0033680079 scopus 로고    scopus 로고
    • Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis
    • Andersen, A. A. & Collins, R. A. (2000). Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis. Mol. Cell, 5, 469-478.
    • (2000) Mol. Cell , vol.5 , pp. 469-478
    • Andersen, A.A.1    Collins, R.A.2
  • 23
    • 0014669561 scopus 로고
    • Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside and their derivatives
    • Ward, D. C., Reich, E. & Stryer, L. (1969). Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside and their derivatives. J. Biol. Chem. 244, 1228-1237.
    • (1969) J. Biol. Chem. , vol.244 , pp. 1228-1237
    • Ward, D.C.1    Reich, E.2    Stryer, L.3
  • 24
    • 0028128641 scopus 로고
    • Melting and premelting transitions of an oligomer measured by DNA base fluorescence and absorption
    • Xu, D., Evans, K. O. & Nordlund, T. M. (1994). Melting and premelting transitions of an oligomer measured by DNA base fluorescence and absorption. Biochemistry, 33, 9592-9599.
    • (1994) Biochemistry , vol.33 , pp. 9592-9599
    • Xu, D.1    Evans, K.O.2    Nordlund, T.M.3
  • 25
    • 0032529485 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence strudies of base stacking interactions at abasic sites in DNA: Metal-ion and base sequence effects
    • Stivers, J. T. (1998). 2-Aminopurine fluorescence strudies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucl. Acids Res. 26, 3837-3844.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 3837-3844
    • Stivers, J.T.1
  • 26
    • 0035793105 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking
    • Jean, J. M. & Hall, K. B. (2001). 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc. Natl Acad. Sci. USA, 98, 37-41.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 37-41
    • Jean, J.M.1    Hall, K.B.2
  • 27
    • 0027493457 scopus 로고
    • Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment
    • Bloom, L. B., Otto, M. R., Beechem, J. M. & Goodman, M. F. (1993). Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment. Biochemistry, 32, 11247-11258.
    • (1993) Biochemistry , vol.32 , pp. 11247-11258
    • Bloom, L.B.1    Otto, M.R.2    Beechem, J.M.3    Goodman, M.F.4
  • 28
    • 0033555454 scopus 로고    scopus 로고
    • Electron transfer between bases in double helical DNA
    • Kelley, S. O. & Barton, J. K. (1999). Electron transfer between bases in double helical DNA. Science, 283, 375-381.
    • (1999) Science , vol.283 , pp. 375-381
    • Kelley, S.O.1    Barton, J.K.2
  • 29
    • 0033215448 scopus 로고    scopus 로고
    • Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
    • Perrotta, A. T., Shih, I. & Been, M. D. (1999). Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science, 286, 123-126.
    • (1999) Science , vol.286 , pp. 123-126
    • Perrotta, A.T.1    Shih, I.2    Been, M.D.3
  • 30
    • 0030747007 scopus 로고    scopus 로고
    • a shift at the active site of a lead-dependent ribozyme
    • a shift at the active site of a lead-dependent ribozyme. J. Am. Chem. Soc. 119, 6621-6628.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 6621-6628
    • Legault, P.1    Pardi, A.2
  • 31
    • 0028855671 scopus 로고
    • Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA
    • Guo, H. C. T. & Collins, R. A. (1995). Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA. EMBO J. 14, 368-376.
    • (1995) EMBO J , vol.14 , pp. 368-376
    • Guo, H.C.T.1    Collins, R.A.2
  • 32
    • 0031215134 scopus 로고    scopus 로고
    • An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
    • Nesbitt, S., Hegg, L. A. & Fedor, M. J. (1997). An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem. Biol. 4, 619-630.
    • (1997) Chem. Biol. , vol.4 , pp. 619-630
    • Nesbitt, S.1    Hegg, L.A.2    Fedor, M.J.3
  • 33
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferré-d' Amaré A. R., Zhou, K. & Doudna, J. A. (1998). Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferré-d' Amaréas, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 34
    • 0029859191 scopus 로고    scopus 로고
    • Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases
    • Peracchi, A., Beigelman, L., Usman, N. & Herschlag, D. (1996). Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases. Proc. Natl Acad. Sci. USA, 93, 11522-11527.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 11522-11527
    • Peracchi, A.1    Beigelman, L.2    Usman, N.3    Herschlag, D.4
  • 35
    • 0032552962 scopus 로고    scopus 로고
    • A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations
    • Peracchi, A., Karpeisky, A., Maloney, L., Beigelman, L. & Herschlag, D. (1998). A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations. Biochemistry, 37, 14765-14775.
    • (1998) Biochemistry , vol.37 , pp. 14765-14775
    • Peracchi, A.1    Karpeisky, A.2    Maloney, L.3    Beigelman, L.4    Herschlag, D.5
  • 36
    • 0031758565 scopus 로고    scopus 로고
    • Structure-function relationships in the hammerhead ribozyme probed by base rescue
    • Peracchi, A., Matulic-Adamic, J., Wang, S., Beigelman, L. & Herschlag, D. (1998). Structure-function relationships in the hammerhead ribozyme probed by base rescue. RNA, 4, 1332-1346.
    • (1998) RNA , vol.4 , pp. 1332-1346
    • Peracchi, A.1    Matulic-Adamic, J.2    Wang, S.3    Beigelman, L.4    Herschlag, D.5
  • 37
    • 0036488944 scopus 로고    scopus 로고
    • The contribution of 2′-hydroxyls to the cleavage activity of the Neurospora VS ribozyme
    • Sood, V. D., Yekta, S. & Collins, R. A. (2002). The contribution of 2′-hydroxyls to the cleavage activity of the Neurospora VS ribozyme. Nucl. Acids Res. 30, 1132-1138.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 1132-1138
    • Sood, V.D.1    Yekta, S.2    Collins, R.A.3
  • 38
    • 49149135789 scopus 로고
    • Deoxy-nucleoside phosphoramidites-a new class of key intermediates for deoxypolynucleotide synthesis
    • Beaucage, S. L. & Caruthers, M. H. (1981). Deoxy-nucleoside phosphoramidites-a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Letters, 22, 1859-1862.
    • (1981) Tetrahedron Letters , vol.22 , pp. 1859-1862
    • Beaucage, S.L.1    Caruthers, M.H.2
  • 39
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan, J. F., Groebe, D. R., Witherall, G. W. & Uhlenbeck, O. C. (1987). Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15, 8783-8798.
    • (1987) Nucl. Acids Res. , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherall, G.W.3    Uhlenbeck, O.C.4
  • 40
    • 0031463467 scopus 로고    scopus 로고
    • Ion-induced folding of the hammerhead ribozyme: A fluorescence resonance energy transfer study
    • Bassi, G. S., Murchie, A. I. H., Walter, F., Clegg, R. M. & Lilley, D. M. J. (1997). Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study. EMBO J. 16, 7481-7489.
    • (1997) EMBO J. , vol.16 , pp. 7481-7489
    • Bassi, G.S.1    Murchie, A.I.H.2    Walter, F.3    Clegg, R.M.4    Lilley, D.M.J.5
  • 41
    • 0029011972 scopus 로고
    • A secondary-structure model for the self-cleaving region of Neurospora VS RNA
    • Beattie, T. L., Olive, J. E. & Collins, R. A. (1995). A secondary-structure model for the self-cleaving region of Neurospora VS RNA. Proc. Natl Acad. Sci. USA, 92, 4686-4690.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 4686-4690
    • Beattie, T.L.1    Olive, J.E.2    Collins, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.