Molecular recognition properties of IGS-mediated reactions catalyzed by a Pneumocystis carinii group I intron

Nucleic Acids Research

Volumn 31, Issue 7, 2003, Pages 1921-1934

  Johnson, Ashley K ^a   Baum, Dana A ^a   Tye, Jesse ^a   Bell, Michael A ^a   Testa, Stephen M ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING PROTEIN; MAGNESIUM CHLORIDE; RIBOZYME; RNA;

BASE PAIRING; CATALYSIS; COMBINATORIAL LIBRARY; CONTROLLED STUDY; CYCLIZATION; EXON; GENE LOCATION; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; INTRON; MISMATCH REPAIR; MOLECULAR RECOGNITION; NONHUMAN; PATHOGENESIS; PNEUMOCYSTIS CARINII; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STABILITY; REVIEW; RNA STRUCTURE; SUICIDE GENE; TETRAHYMENA; THERMODYNAMICS;

BASE SEQUENCE; BINDING, COMPETITIVE; DNA, FUNGAL; EXONS; INTRONS; KINETICS; MAGNESIUM CHLORIDE; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; PNEUMOCYSTIS; RNA SPLICING; RNA, CATALYTIC; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

PNEUMOCYSTIS CARINII; PROTOZOA; TETRAHYMENA;

EID: 0037388052     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg280     Document Type: Review

References (53)

1. Kruger,K., Grabowski,P.J., Zaug,A.J., Sands,J., Gottschling,D.E. and Cech,T.R. (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31, 147-157.
2. Zaug,A.J., Grabowski,P.J. and Cech,T.R. (1983) Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. Nature, 301, 578-583.
3. Zaug,A.J., Kent,J.R. and Cech,T.R. (1984) A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA. Science, 224, 574-578.
4. Zaug,A.J., Been,M.D. and Cech,T.R. (1986) The Tetrahymena ribozyme acts like an RNA restriction endonuclease. Nature, 324, 429-433.
5. Zaug,A.J. and Cech,T.R. (1986) The intervening sequence RNA of Tetrahymena is an enzyme. Science, 231, 470-475.
6. Testa,S.M., Haidaris,C.G., Gigliotti,F. and Turner,D.H. (1997) A Pneumocystis carinii group I intron ribozyme that does not require 2′ OH groups on its 5′ exon mimic for binding to the catalytic core. Biochemistry, 36, 15303-15314.
7. Bevilacqua,P.C., Kierzek,R., Johnson,K.A. and Turner,D.H. (1992) Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science, 258, 1355-1358.
8. Herschlag,D. (1992) Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme. Biochemistry, 31, 1386-1399.
9. Waring,R.B., Scazzocchio,C., Brown,T.A. and Davies,R.W. (1983) Close relationship between certain nuclear and mitochondrial introns. Implications for the mechanism of RNA splicing. J. Mol. Biol., 167, 595-605.
10. Been,M.D. and Cech,T.R. (1986) One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. Cell, 47, 207-216.
11. 2+ binding interactions. Nucleic Acids Res., 17, 355-371.
12. Pyle,A.M. and Cech,T.R. (1991) Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups. Nature, 350, 628-631.
13. Bevilacqua,P.C. and Turner,D.H. (1991) Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: evidence for ribozyme specific interactions with 2′ OH groups. Biochemistry, 30, 10632-10640.
14. Murphy,F.L. and Cech,T.R. (1989) Alteration of substrate specificity for the endoribonucleolytic cleavage of RNA by the Tetrahymena ribozyme. Proc. Natl Acad. Sci. USA, 86, 9218-9222.
15. Sullenger,B.A. and Cech,T.R. (1994) Ribozyme-mediated repair of defective mRNA by targeted, trans-splicing. Nature, 371, 619-622.
16. Sargueil,B. and Tanner,N.K. (1993) A shortened form of the Tetrahymena thermophila group I intron can catalyze the complete splicing reaction in trans. J. Mol. Biol., 233, 629-643.
17. Lan,N., Howrey,R.P., Lee,S.W., Smith,C.A. and Sullenger,B.A. (1998) Ribozyme-mediated repair of sickle beta-globin mRNAs in erythrocyte precursors. Science, 280, 1593-1596.
18. Phylactou,L.A., Darrah,C. and Wood,M.J. (1998) Ribozyme-mediated trans-splicing of a trinucleotide repeat. Nature Genet., 18, 378-381.
19. Kohler,U., Ayre,B.G., Goodman,H.M. and Haseloff,J. (1999) Trans-splicing ribozymes for targeted gene delivery. J. Mol. Biol., 285, 1935-1950.
20. Zarrinkar,P.P. and Sullenger,B.A. (1999) Optimizing the substrate specificity of a group I intron ribozyme. Biochemistry, 38, 3426-3432.
21. Watanabe,T. and Sullenger,B.A. (2000) Induction of wild-type p53 activity in human cancer cells by ribozymes that repair mutant p53 transcripts. Proc. Natl Acad. Sci. USA, 97, 8490-8494.
22. Bell,M.A., Johnson,A.K. and Testa,S.M. (2002) Ribozyme-catalyzed excision of targeted sequences from within RNAs. Biochemistry, 41, 15327-15333.
23. Testa,S.M., Gryaznov,S.M. and Turner,D.H. (1999) In vitro suicide inhibition of self-splicing of a group I intron from Pneumocystis carinii by an N3′→P5′ phosphoramidate hexanucleotide. Proc. Natl Acad. Sci. USA, 96, 2734-2739.
24. Disney,M.D., Testa,S.M. and Turner,D.H. (2000) Targeting a Pneumocystis carinii group I intron with methylphosphonate oligonucleotides: backbone charge is not required for binding or reactivity. Biochemistry, 39, 6991-7000.
25. Disney,M.D., Matray,T., Gryaznov,S.M. and Turner,D.H. (2001) Binding enhancement by tertiary interaction and suicide inhibition of a Candida albicans group I intron by phosphoramidate and 2′-O-methyl hexanucleotides. Biochemistry, 40, 6520-6526.
26. Sullivan,F.X. and Cech,T.R. (1985) Reversibility of cyclization of the Tetrahymena rRNA intervening sequence: implication for the mechanism of splice site choice. Cell, 42, 639-648.
27. 2+ concentrations. Biochemistry, 27, 6384-6392.
28. Disney,M.D., Gryaznov,S.M. and Turner,D.H. (2000) Contributions of individual nucleotides to tertiary binding of substrate by a Pneumocystis carinii group I intron. Biochemistry, 39, 14269-14278.
29. Testa,S.M., Gryaznov,S.M. and Turner,D.H. (1998) Antisense binding enhanced by tertiary interactions: binding of phosphorothioate and N3′→P5′ phosphoramidate hexanucleotides to the catalytic core of a group I ribozyme from the mammalian pathogen Pneumocystis carinii. Biochemistry, 37, 9379-9385.
30. Gryaznov,S.M. and Letsinger,R.L. (1992) Synthesis and properties of oligonucleotides containing aminodeoxythymidine units. Nucleic Acids Res., 20, 3403-3409.
31. Gryaznov,S.M., Lloyd,D.H., Chen,J.K., Schultz,R.G., DeDionisio,L.A., Ratmeyer,L. and Wilson,W.D. (1995) Oligonucleotide N3′→P5′ phosphoramidates. Proc. Natl Acad. Sci. USA, 92, 5798-5802.
32. Zaug,A.J., Grosshan,C.A. and Cech,T.R. (1988) Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry, 27, 8924-8931.
33. Been,M.D. and Cech,T.R. (1987) Selection of circularization sites in a group I IVS RNA requires multiple alignments of an internal template-like sequence. Cell, 50, 951-961.
34. Roman,J. and Woodson,S.A. (1995) Reverse splicing of the Tetrahymena IVS: evidence for multiple reaction sites in the 23S rRNA. RNA, 1, 478-490.
35. Jones,J.T., Lee,S.W. and Sullenger,B.A. (1996) Tagging ribozyme reaction sites to follow trans-splicing in mammalian cells. Nature Med., 2, 643-648.
36. Roman,J. and Woodson,S.A. (1998) Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo. Proc. Natl Acad. Sci. USA, 95, 2134-2139.
37. Roman,J., Rubin,M.N. and Woodson,S.A. (1999) Sequence specificity of in vivo reverse splicing of the Tetrahymena group I intron. RNA, 5, 1-13.
38. Harrison,P.M. and Hoare,R.J. (1980) Metals in Biochemistry. Chapman & Hall, New York, pp. 8-9.
39. Macquire,M.E. (1990) In Sigel,H. and Sigel,A (eds), Metals in Biological Systems. Dekker, New York, Vol. 26, pp. 135-153.
40. Weeks,K.M. and Cech,T.R. (1995) Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5′ splice site domain. Cell, 82, 221-230.
41. Herschlag,D. (1991) Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc. Natl Acad. Sci. USA, 88, 6921-6925.
42. Strobel,S.A. and Cech,T.R. (1995) Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site. Science, 267, 675-679.
43. Soukup,J.K., Minakawa,N., Matsuda,A. and Strobel,S.A. (2002) Identification of A-minor interactions within a bacterial group I intron active site by 3-deazaadenosine interference mapping. Biochemistry, 41, 10426-10438.
44. Battle,D.J. and Doudna,J.A. (2002) Specificity of RNA-RNA helix recognition. Proc. Natl Acad. Sci. USA, 99, 11676-11681.
45. Doudna,J.A., Cormack,B.P. and Szostak,J.W. (1989) RNA structure, not sequence, determines the 5′ splice-site specificity of a group I intron. Proc. Natl Acad. Sci. USA, 86, 7402-7406.
46. Campbell,T.B. and Cech,T.R. (1996) Mutations in the Tetrahymena ribozyme internal guide sequence: effects on docking of the P1 helix into the catalytic core and correlation with catalytic activity. Biochemistry, 35, 11493-11502.
47. Doherty,E.A., Batey,R.T., Masquida,B. and Doudna,J.A. (2001) A universal mode of helix packing in RNA. Nature Struct. Biol., 8, 339-343.
48. Been,M.D. and Cech,T.R. (1987) Selection of circularization sites in a group I IVS RNA requires multiple alignments of an internal template-like sequence. Cell, 50, 951-961.
49. Strobel,S.A. and Cech,T.R. (1994) Translocation of an RNA duplex on a ribozyme. Nature Struct. Biol., 1, 13-17.
50. Cech,T.R. (1990) Self-splicing of group I introns. Annu. Rev. Biochem., 59, 543-568.
51. Roberts,R.W. and Crothers,D.M. (1991) Specificity and stringency in DNA triplex formation. Proc. Natl Acad. Sci. USA, 88, 9397-9401.
52. Woolf,T.M., Melton,D.A. and Jennings,C.G.B. (1992) Specificity of antisense oligonucleotides in vivo. Proc. Natl Acad. Sci. USA, 89, 7305-7309.
53. Pyle,A.M., McSwiggen,J.A. and Cech,T.R. (1990) Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena. Proc. Natl Acad. Sci. USA, 87, 8187-8191.