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Volumn 32, Issue 21, 2004, Pages 6240-6250

The role of phosphate groups in the VS ribozyme-substrate interaction

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; LIGAND; MAGNESIUM ION; MANGANESE; METAL ION; NUCLEOTIDE; ORGANOPHOSPHATE; PHOSPHATE; PHOSPHOROTHIOIC ACID; RIBOZYME; URACIL;

EID: 13444279054     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh957     Document Type: Article
Times cited : (9)

References (43)
  • 2
    • 0029011972 scopus 로고
    • A secondary-structure model for the self-cleaving region of Neurospora VS RNA
    • Beattie,T.L., Olive,J.E. and 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
  • 3
    • 0028855671 scopus 로고
    • Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA
    • Guo,H.C.T. and 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
  • 4
    • 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. and 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
  • 5
    • 0033680079 scopus 로고    scopus 로고
    • Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis
    • Andersen,A.A. and 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
  • 6
    • 0034940798 scopus 로고    scopus 로고
    • Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme
    • Andersen,A.A. and Collins,R.A. (2001) Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme. Proc. Natl Acad. Sci. USA, 98, 7730-7735.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 7730-7735
    • Andersen, A.A.1    Collins, R.A.2
  • 8
    • 0034967913 scopus 로고    scopus 로고
    • A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA
    • Flinders,J. and Dieckmann,T. (2001) A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA. J. Mol. Biol., 308, 665-679.
    • (2001) J. Mol. Biol. , vol.308 , pp. 665-679
    • Flinders, J.1    Dieckmann, T.2
  • 9
    • 0034538971 scopus 로고    scopus 로고
    • Structure of the ribozyme substrate hairpin of Neurospora VS RNA: A close look at the cleavage site
    • Michiels,P.J.A., Schouten,C.H.J., Hilbers,C.W. and Heus,H.A. (2000) Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site. RNA, 6, 1821-1832.
    • (2000) RNA , vol.6 , pp. 1821-1832
    • Michiels, P.J.A.1    Schouten, C.H.J.2    Hilbers, C.W.3    Heus, H.A.4
  • 10
    • 0035476689 scopus 로고    scopus 로고
    • Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme
    • Hiley,S.L. and Collins,R.A. (2001) Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme. EMBO J, 20, 5461-5469.
    • (2001) EMBO J. , vol.20 , pp. 5461-5469
    • Hiley, S.L.1    Collins, R.A.2
  • 11
    • 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. and 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
  • 12
    • 0037093486 scopus 로고    scopus 로고
    • The global structure of the VS ribozyme
    • Lafontaine,D.A., Norman,D.G. and 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
  • 13
    • 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. and 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
  • 14
    • 0037009368 scopus 로고    scopus 로고
    • 4-thio-U cross-linking identifies the active site of the VS ribozyme
    • Hiley,S.L., Sood,V.D., Fan,J. and Collins,R.A. (2002) 4-thio-U cross-linking identifies the active site of the VS ribozyme. EMBO J, 21, 4691-4698.
    • (2002) EMBO J. , vol.21 , pp. 4691-4698
    • Hiley, S.L.1    Sood, V.D.2    Fan, J.3    Collins, R.A.4
  • 15
    • 0036396544 scopus 로고    scopus 로고
    • Functional group requirements in the probable active site of the VS ribozyme
    • Lafontaine,D.A., Wilson,T.J., Zhao,Z.-Y. and Lilley,D.M.J. (2002) Functional group requirements in the probable active site of the VS ribozyme. J. Mol. Biol., 323, 23-34.
    • (2002) J. Mol. Biol. , vol.323 , pp. 23-34
    • Lafontaine, D.A.1    Wilson, T.J.2    Zhao, Z.-Y.3    Lilley, D.M.J.4
  • 16
    • 0037446518 scopus 로고    scopus 로고
    • Ionisation of a critical adenosine residue in the Neurospora Varkud satellite ribozyme active site
    • Jones,F.D. and Strobel,S.A. (2003) Ionisation of a critical adenosine residue in the Neurospora Varkud satellite ribozyme active site. Biochemistry, 42, 4265-4276.
    • (2003) Biochemistry , vol.42 , pp. 4265-4276
    • Jones, F.D.1    Strobel, S.A.2
  • 17
    • 0036488944 scopus 로고    scopus 로고
    • The contribution of 2′-hydoxyls to the cleavage activity of the Neurospora VS ribozyme
    • Sood,V.D., Yekta,S. and Collins,R.A. (2002) The contribution of 2′-hydoxyls to the cleavage activity of the Neurospora VS ribozyme. Nucleic Acids Res., 30, 1132-1138.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1132-1138
    • Sood, V.D.1    Yekta, S.2    Collins, R.A.3
  • 18
    • 0036440685 scopus 로고    scopus 로고
    • The role of magnesium ions and 2′-hydroxyl groups in the VS ribozyme-substrate interaction
    • Tzokov,S.B., Murray,I.A. and Grasby,J.A. (2002) The role of magnesium ions and 2′-hydroxyl groups in the VS ribozyme-substrate interaction. J. Mol. Biol., 324, 215-226.
    • (2002) J. Mol. Biol. , vol.324 , pp. 215-226
    • Tzokov, S.B.1    Murray, I.A.2    Grasby, J.A.3
  • 19
    • 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. and 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
  • 20
    • 0030967825 scopus 로고    scopus 로고
    • Metal ions play a passive role in the hairpin ribozyme catalysed reaction
    • Young,K.J., Gill,F. and Grasby,J.A. (1997) Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucleic Acids Res., 25, 3760-3766.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3760-3766
    • Young, K.J.1    Gill, F.2    Grasby, J.A.3
  • 21
    • 0036219133 scopus 로고    scopus 로고
    • RNA footprinting analysis using ion pair reverse phase liquid chromatography
    • Dickman,M.J., Conroy,M.J., Grasby,J.A. and Hornby,D.P. (2002) RNA footprinting analysis using ion pair reverse phase liquid chromatography. RNA, 8, 247-251.
    • (2002) RNA , vol.8 , pp. 247-251
    • Dickman, M.J.1    Conroy, M.J.2    Grasby, J.A.3    Hornby, D.P.4
  • 22
    • 13444269065 scopus 로고    scopus 로고
    • Real time kinetics of ribozyme reactions
    • Krupp,G. and Gaur,R.K. (eds.), Eaton Publishing, Narwick, MA
    • Singh,K.K., Parwaresch,R. and Krupp,G. (2000) Real time kinetics of ribozyme reactions. In Krupp,G. and Gaur,R.K. (eds.), Ribozyme Biochemistry and Biotechnology. Eaton Publishing, Narwick, MA, pp. 351-370.
    • (2000) Ribozyme Biochemistry and Biotechnology , pp. 351-370
    • Singh, K.K.1    Parwaresch, R.2    Krupp, G.3
  • 23
    • 0034651754 scopus 로고    scopus 로고
    • RNA double cleavage by a hairpin-derived twin ribozyme
    • Schmidt,C., Welz,R. and Muller,S. (2000) RNA double cleavage by a hairpin-derived twin ribozyme. Nucleic Acids Res., 28, 886-894.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 886-894
    • Schmidt, C.1    Welz, R.2    Muller, S.3
  • 24
    • 3843111134 scopus 로고    scopus 로고
    • The synthesis and properties of oligoribonucleotide-spermine conjugates
    • Marsh,A., Williams,D.M. and Grasby,J.A. (2004) The synthesis and properties of oligoribonucleotide-spermine conjugates. Organic and Biomolecular Chemistry, 2, 2103-2112.
    • (2004) Organic and Biomolecular Chemistry , vol.2 , pp. 2103-2112
    • Marsh, A.1    Williams, D.M.2    Grasby, J.A.3
  • 25
    • 0031828144 scopus 로고    scopus 로고
    • Hammerhead ribozyme kinetics
    • Stage-Zimmerman,T.K. and Uhlenbeck,O.C. (1998) Hammerhead ribozyme kinetics. RNA, 4, 875-889.
    • (1998) RNA , vol.4 , pp. 875-889
    • Stage-Zimmerman, T.K.1    Uhlenbeck, O.C.2
  • 26
    • 0030920270 scopus 로고    scopus 로고
    • Kinetic mechanism of the hairpin ribozyme
    • Esteban,J.A., Banerjee,A.R. and Burke,J.M. (1997) Kinetic mechanism of the hairpin ribozyme. J. Biol. Chem., 272, 13629-13639.
    • (1997) J. Biol. Chem. , vol.272 , pp. 13629-13639
    • Esteban, J.A.1    Banerjee, A.R.2    Burke, J.M.3
  • 27
    • 0025265468 scopus 로고
    • Substrate sequence effects on 'hammerhead' RNA catalytic efficiency
    • Fedor,M.J. and Uhlenbeck,O.C. (1990) Substrate sequence effects on 'hammerhead' RNA catalytic efficiency. Proc. Natl Acad. Sci. USA, 87, 1668-1672.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 1668-1672
    • Fedor, M.J.1    Uhlenbeck, O.C.2
  • 28
    • 0942279692 scopus 로고    scopus 로고
    • Efficient, pH-dependent RNA ligation by the VS ribozyme in trans
    • McLeod,A.C. and Lilley,D.M.J. (2004) Efficient, pH-dependent RNA ligation by the VS ribozyme in trans. Biochemistry, 43, 1118-1125.
    • (2004) Biochemistry , vol.43 , pp. 1118-1125
    • McLeod, A.C.1    Lilley, D.M.J.2
  • 30
    • 0035945247 scopus 로고    scopus 로고
    • An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5′ and 3′-termini
    • Jones,F.D., Ryder,S.P. and Strobel,S.A. (2001) An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5′ and 3′-termini. Nucleic Acids Res., 29, 5115-5120.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 5115-5120
    • Jones, F.D.1    Ryder, S.P.2    Strobel, S.A.3
  • 31
    • 0036760718 scopus 로고    scopus 로고
    • Developments in RNA chemistry, a personal view
    • Eckstein,F. (2002) Developments in RNA chemistry, a personal view. Biochimie, 84, 841-848.
    • (2002) Biochimie , vol.84 , pp. 841-848
    • Eckstein, F.1
  • 32
    • 0032707136 scopus 로고    scopus 로고
    • Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain
    • Basu,S. and Strobel,S.A. (1999) Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain. RNA, 5, 1399-1407.
    • (1999) RNA , vol.5 , pp. 1399-1407
    • Basu, S.1    Strobel, S.A.2
  • 33
    • 0034081812 scopus 로고    scopus 로고
    • An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction
    • Shan,S.-O. and Herschlag,D. (2000) An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction. RNA, 6, 795-813.
    • (2000) RNA , vol.6 , pp. 795-813
    • Shan, S.-O.1    Herschlag, D.2
  • 34
    • 0027416218 scopus 로고
    • Reaction conditions and kinetics of self-cleavage of a ribozyme derived from Neurospora VS RNA
    • Collins,R.A. and Olive,J.E. (1993) Reaction conditions and kinetics of self-cleavage of a ribozyme derived from Neurospora VS RNA. Biochemistry, 32, 2795-2799.
    • (1993) Biochemistry , vol.32 , pp. 2795-2799
    • Collins, R.A.1    Olive, J.E.2
  • 35
    • 0022418143 scopus 로고
    • Bond order and charge localization in nucleoside phosphorothioates
    • Frey,P.A. and Sammons,R.D. (1985) Bond order and charge localization in nucleoside phosphorothioates. Science, 228, 541-545.
    • (1985) Science , vol.228 , pp. 541-545
    • Frey, P.A.1    Sammons, R.D.2
  • 36
    • 0000991444 scopus 로고
    • Phosphorus-oxygen bond order in adenosine 5′-O-phosphorothioate dianion
    • Iyengar,R., Eckstein,F. and Frey,P.A. (1984) Phosphorus-oxygen bond order in adenosine 5′ -O-phosphorothioate dianion. J. Am. Chem. Soc., 106, 8309-8310.
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 8309-8310
    • Iyengar, R.1    Eckstein, F.2    Frey, P.A.3
  • 37
    • 0027247579 scopus 로고
    • Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena
    • Christian,E.L. and Yarus,M. (1993) Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena. Biochemistry, 32, 4475-4480.
    • (1993) Biochemistry , vol.32 , pp. 4475-4480
    • Christian, E.L.1    Yarus, M.2
  • 38
    • 0024554271 scopus 로고
    • Determination of RNA-Protein contacts using thiophosphate substitutions
    • Milligan,J.F. and Uhlenbeck,O.C. (1989) Determination of RNA-Protein contacts using thiophosphate substitutions. Biochemistry 28, 2849-2855.
    • (1989) Biochemistry , vol.28 , pp. 2849-2855
    • Milligan, J.F.1    Uhlenbeck, O.C.2
  • 39
    • 0028252696 scopus 로고
    • Ribonuclease revisited: Catalysis via the classical general acid-base mechanism of a triester-like mechanism
    • Herschlag,D. (1994) Ribonuclease revisited: catalysis via the classical general acid-base mechanism of a triester-like mechanism. J. Am. Chem. Soc., 116, 11631-11635.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 11631-11635
    • Herschlag, D.1
  • 40
    • 0037073473 scopus 로고    scopus 로고
    • Rearrangement of substrate secondary structure facilitates binding to the Neurospora VS ribozyme
    • Zamel,R. and Collins,R.A. (2002) Rearrangement of substrate secondary structure facilitates binding to the Neurospora VS ribozyme. J. Mol. Biol., 324, 903-915.
    • (2002) J. Mol. Biol. , vol.324 , pp. 903-915
    • Zamel, R.1    Collins, R.A.2
  • 41
    • 0032571245 scopus 로고    scopus 로고
    • Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates
    • Brautigam,C.A. and Steitz,T.A. (1998) Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J. Mol. Biol., 277, 363-377.
    • (1998) J. Mol. Biol. , vol.277 , pp. 363-377
    • Brautigam, C.A.1    Steitz, T.A.2
  • 42
    • 0032192761 scopus 로고    scopus 로고
    • The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
    • Murray,J.B., Seyhan,A.A., Walter,N.G., Burke,J.M. and Scott,W.G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chemistry & Biology, 5, 587-595.
    • (1998) Chemistry & Biology , vol.5 , pp. 587-595
    • Murray, J.B.1    Seyhan, A.A.2    Walter, N.G.3    Burke, J.M.4    Scott, W.G.5
  • 43
    • 0018796264 scopus 로고
    • Diastereoisomers of 5′-O-adenosyl-3′-O-uridyl phosphorothioate: Chemical synthesis and enzymatic properties
    • Burgers,P.M.J. and Eckstein,F. (1979) Diastereoisomers of 5′-O-adenosyl-3′-O-uridyl phosphorothioate: chemical synthesis and enzymatic properties. Biochemistry, 18, 592-596.
    • (1979) Biochemistry , vol.18 , pp. 592-596
    • Burgers, P.M.J.1    Eckstein, F.2


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