Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities

Journal of Molecular Biology

Volumn 267, Issue 1, 1997, Pages 163-171

  Liu, Qiaolian ^a   Green, Justin B ^a   Khodadadi, Arbi ^a   Haeberli, Peter ^b   Beigelman, Leonid ^b   Pyle, Anna Marie ^a  

^a The New York Presbyterian Hospital   (United States)

^b Sirna Therapeutics Inc   (United States)

Author keywords

Base flipping; Ribozyme; RNA catalysis; RNA folding; Self splicing

Indexed keywords

ADENINE; ADENOSINE; NUCLEIC ACID BASE;

ARTICLE; INTRON; MOLECULAR RECOGNITION; MUTAGENESIS; PRIORITY JOURNAL; RNA SPLICING; STEREOCHEMISTRY;

EID: 0031582058     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0845     Document Type: Article

References (41)

1. Beigelman L., Karpeisky A., Usman N. Synthesis of 1-deoxy- D -ribofuranose phosphoramidite & the incorporation of abasic nucleotides in stem-loop II of a hammerhead ribozyme. Biorg. Med. Chem. Letters. 4:1994;1715-1720.
2. Boulanger S. C., Belcher S. M., Schmidt U., Dib-Hajj S. D., Schmidt T., Perlman P. S. Studies of point mutants define three essential paired nucleotides in the domain 5 substructure of a group II intron. Mol. Cell. Biol. 15:1995;4479-4488.
3. Chanfreau G., Jacquier A. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J. 15:1996;3466-3476.
4. Cheng X., Blumenthal R. M. Finding a basis for flipping bases. Structure. 4:1996;639-645.
5. Chin K., Pyle A. M. Branch-point attack in group II introns is a highly reversible transesterification, providing a possible proof-reading mechanism for 5′-splice site selection. RNA. 1:1995;391-406.
6. Daniels D., Michels W. J., Pyle A. M. Two competing pathways for self-splicing by group II introns; a quantitative analysis of in-vitro reaction rates and products. J. Mol. Biol. 256:1996;31-49.
7. Dib-Hajj S. D., Boulanger S. C., Hebbar S. K., Peebles C. L., Franzen J. S., Perlman P. S. Domain 5 interacts with Domain 6 and influences the second transesterification reaction of group II intron self-splicing. Nucl. Acids Res. 21:1993;1797-1804.
8. Doudna J. A., Szostak J. W., Rich A., Usman N. Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function. J. Org. Chem. 55:1990;5547-5549.
9. Ferat J.-L., Michel F. Group II self-splicing introns in bacteria. Nature. 364:1193;358-361.
10. Ferat J.-L., Le Gouar M., Michel F. Multiple group II self-splicing introns in mobile DNA from Escherichia coli. C.R. Acad. Sci. Paris, Life Sci. 317:1994;141-148.
11. Fu D.-J., Rajur S. B., McLaughlin L. W. Importance of specific guanosine N7-nitrogens and purine amino groups for efficient cleavage by hammerhead ribozyme. Biochemistry. 32:1993;10629-10637.
12. Green R., Szostak J. W., Benner S., Rich A., Usman N. Synthesis of RNA containing inosine: analysis of the sequence requirements for the 5′ splice site of theTetrahymena group I intron. Nucl. Acids Res. 15:1991;4161-4166.
13. Hornig H., Aebi M., Weissman C. Effect of mutation at the lariat branch acceptor site on β-globin pre-mRNA splicing in vitro. Nature. 324:1986;589-591.
14. Jacquier A., Jacquesson-Breuleux N. Splice site selection and role of the lariat in a Group II intron. J. Mol. Biol. 219:1991;415-428.
15. Jarrell K. A., Dietrich R. C., Perlman P. S. Group II intron domain 5 facilitates a trans-splicing reaction. Mol. Cell. Biol. 8:1988a;2361-2366.
16. Jarrell K. A., Peebles C. L., Dietrich R. C., Romiti S. L., Perlman P. S. Group II intron self-splicing: alternative reaction conditions yield novel products. J. Biol. Chem. 263:1988b;3432-3439.
17. Jencks W. P. Catalysis in Chemistry and Enzymology. 1987;Dover, New York.
18. Konarska M. M., Grabowski P. J., Padgett R. A., Sharp P. S. Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature. 313:1985;552-557.
19. Kunkel T. A., Bebenek K., McClary J. Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol. 204:1991;125-139.
20. Michel F., Ferat J.-L. Structure and activities of group II introns. Annu. Rev. Biochem. 64:195;435-461.
21. Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns-a review. Gene. 82:1989;5-30.
22. Moore M. J., Sharp P. A. Site-specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites. Science. 256:1992;992-997.
23. Moore M. J., Sharp P. A. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature. 365:1993;364-368.
24. Moore M. J., Query C. C., Sharp P. A. Splicing of precursors to messenger RNAs by the spliceosome. The RNA World. 1993;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
25. Padgett R. A., Konarska M. M., Grabowski P. J., Hardy S. F., Sharp P. A. Lariat RNAs as intermediates and products in the splicing of messenger RNA precursors. Science. 225:1984;898-903.
26. Peebles C. L., Perlman P. S., Mecklenburg K. L., Petrillo M. L., Tabor J. H., Jarrell K. A., Cheng H.-L. A self-splicing RNA excises an intron lariat. Cell. 44:1986;213-223.
27. Portmann S., Grimm S., Workaman C., Usman N., Egli M. Crystal structures of an A-form duplex with single-adenosine bulges: a conformational basis for site-specific RNA self-cleavage. Chem. Biol. 3:1996;173-184.
28. Pyle A. M. Catalytic reaction mechanisms and structural features of group II intron ribozymes. Nucleic Acids and Molecular Biology. 1996;New York, Springer Verlag, New York.
29. Query C. C., Moore M. M., Sharp P. A. Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Genes Dev. 8:1994;587-597.
30. Query C. C., Strobel S. A., Sharp P. A. Three recognition events at the branch-site adenine. EMBO J. 15:1996;1392-1402.
31. Reilly J. D., Wallace J. C., Melhem R. F., Kopp D. W., Edmonds M. Isolation and characterization of branched oligonucleotides from RNA. Methods Enzymol. 180:1989;177-191.
32. Ruskin B., Krainer A. R., Maniatis T., Green M. R. Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell. 38:1984;317-331.
33. Schmelzer C., Müller M. W. Self-splicing of group II introns in vitro: lariat formation and 3′-splice site selection in mutant RNAs. Cell. 51:1987;753-762.
34. Schmelzer C., Schweyen R. J. Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation. Cell. 46:1986;557-565.
35. Strobel S. A., Cech T. R., Usman N., Beigelman L. The 2,6-diaminopurine riboside·5-methylisocytidine wobble base pair: an isoenergetic substitution for study of G·U pairs in RNA. Biochemistry. 33:1994;13824-13835.
36. van der Veen R., Arnberg A. C., van der Horst G., Bonen L., Tabak H. F., Grivell L. A. Excised Group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell. 44:1986;225-234.
37. van der Veen R., Kwakman J. H. J. M., Grivell L. A. Mutations at the lariat acceptor site allow self-splicing of a Group II intron without lariat formation. EMBO J. 6:1987;3827-3831.
38. Vijayraghavan U., Parker R., Tamm J., Iimura Y., Rossi J., Abelson J., Guthrie C. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathways, particularly assembly of the spliceosome. EMBO J. 5:1986;1683-1695.
39. Wincott F., DiRenzo A., Shaffer C., Grimm S., Tracz D., Workman C., Sweedler D., Gonzalez C., Scaringe S., Usman N. Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucl. Acids Res. 23:1995;2677-2684.
40. Yang J., Zimmerly S., Perlman P. S., Lambowitz A. M. Efficient integration of an intron RNA into double-stranded DNA by reverse-splicing. Nature. 381:1996;332-335.
41. Zimmerly S., Guo H., Eskes R., Yang J., Perlman P. S., Lambowitz A. M. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell. 83:1995;529-538.