Analysis of catalytic RNA structure and function by nucleotide analog interference mapping

Methods in Molecular Biology

Volumn 848, Issue , 2012, Pages 275-296

  Basu, Soumitra ^a   Morris, Mark J ^a   Pazsint, Catherine ^a  

^a KENT STATE UNIVERSITY   (United States)

Author keywords

Nucleotide analog interference mapping; Ribozyme; RNA structure and function

Indexed keywords

NUCLEOTIDE; RIBOZYME;

ARTICLE; CHEMISTRY; ENZYMOLOGY; GENETIC ENGINEERING; GENETIC TRANSCRIPTION; GENETICS; INTRON; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; TETRAHYMENA;

BASE SEQUENCE; GENETIC ENGINEERING; INTRONS; NUCLEOTIDES; RNA, CATALYTIC; TETRAHYMENA; TRANSCRIPTION, GENETIC;

EID: 84858219997     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-545-9_17     Document Type: Article

References (44)

1. Conway, L., and Wickens, M. (1989) Modification interference analysis of reactions using RNA substrates. Methods Enzymol. 180, 369-379. (Pubitemid 20039586)
2. Stern, S., Moazed, D., and Noller, H. F. (1988) Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164, 481-489. (Pubitemid 19067612)
3. Conrad, F., Hanne, A., Gaur, R. K., and Krupp, G. (1995) Enzymatic synthesis of 2 ¢-modified nucleic acids: Identification of important phosphate and ribose moieties in RNASE P substrates. Nucleic Acids Res. 23, 1845-1853.
4. Gaur, R. K., and Krupp, G. (1993) Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme. Nucleic Acids Res. 21, 21-26. (Pubitemid 23146288)
5. Gish, G., and Eckstein, F. (1988) DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240, 1520-1522.
6. Suydam, I. T., and Strobel, S. A. (2009) Nucleotide analog interference mapping, in Methods Enzymol. 468, 3-30.
7. Strauss-Soukup, J. K., and Strobel, S. A. (2000) A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme. J. Mol. Biol. 302, 339-358.
8. Strobel, S. A., and Shetty, K. (1997) Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc. Natl. Acad. Sci. U. S. A. 94, 2903-2908. (Pubitemid 27157237)
9. Boudvillain, M., and Pyle, A. M. (1998) Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. EMBO J. 17, 7091-7104. (Pubitemid 28550302)
10. Siew, D., Zahler, N. H., Cassano, A. G., Strobel, S. A., and Harris, M. E. (1999) Identification of adenosine functional groups involved in substrate binding by the ribonuclease P ribozyme. Biochemistry 38, 1873-1883.
11. Ryder, S. P., and Strobel, S. A. (1999) Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation. J. Mol. Biol. 291, 295-311. (Pubitemid 29381429)
12. Oyelere, A. K., Kardon, J. R., and Strobel, S. A. (2002) pK a perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping. Biochemistry 41, 3667-3675. (Pubitemid 34224679)
13. Jones, F. D., and Strobel, S. A. (2003) Ionization of a critical adenosine residue in the neurospora varkud satellite ribozyme active site. Biochemistry 42, 4265-4276. (Pubitemid 36418319)
14. Basu, S., Rambo, R. P., Strauss-Soukup, J., Cate, J. H., Ferre-D'Amare, A. R., Strobel, S. A., and Doudna, J. A. (1998) A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat. Struct. Biol. 5, 986-992. (Pubitemid 28506632)
15. Wrzesinski, J., and Jozwiakowski, S. K. (2008) Structural basis for recognition of Co 2+ by RNA aptamers. FEBS J. 275, 1651-1662. (Pubitemid 351463984)
16. 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. (Pubitemid 29530484)
17. Cate, J. H., Hanna, R. L., and Doudna, J. A. (1997) A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol. 4, 553-558. (Pubitemid 27282151)
18. Jansen, J. A., McCarthy, T. J., Soukup, G. A., and Soukup, J. K. (2006) Backbone and nucleobase contacts to glucosamine-6-phosphate in the glm S ribozyme. Nat. Struct. Biol. 13, 517-523. (Pubitemid 43848906)
19. Ryder, S. P., Ortoleva-Donnelly, L., Kosek, A. B., and Strobel, S. A. (2000) Chemical probing of RNA by nucleotide analog interference mapping. Methods Enzymol. 317, 92-109. (Pubitemid 30418079)
20. Arabshahi, A., and Frey, P. A. (1994) A simplified procedure for synthesizing nucleoside 1-thiotriphosphates: dATP a S, dGTP a S, UTP a S, and dTTP a S. Biochem. Biophys. Res. Commun. 204, 150-155. (Pubitemid 24335274)
21. Oyelere, A. K., and Strobel, S. A. (2000) Biochemical detection of cytidine protonation within RNA. J. Am. Chem. Soc. 122, 10259-10267.
22. Eckstein, F., and Goody, R. S. (1976) Synthesis and properties of diastereoisomers of adenosine 5 ¢-(O-1-thiotriphosphate) and adenosine 5 ¢-(O-2-thiotriphosphate). Biochemistry 15, 1685-1691.
23. Chen, J. T., and Benkovic, S. J. (1983) Synthesis and separation of diastereomers of deoxynucleoside 5 ¢-O-(1-thio)triphosphates. Nucleic Acids Res. 11, 3737-3751.
24. Chamberlain, M., Kingston, R., Gilman, M., Wiggs, J., and de Vera, A. (1983) Isolation of bacterial and bacteriophage RNA polymerases and their use in synthesis of RNA in vitro. Methods Enzymol. 101, 540-568. (Pubitemid 13071069)
25. Griffiths, A. D., Potter, B. V. L., and Eperon, I. C. (1987) Stereospecificity of nucleases towards phosphorothioate-substituted RNA: stereochemistry of transcription by T7 RNA polymerase. Nucleic Acids Res. 15, 4145-4162.
26. Sousa, R. (2000) Use of T7 RNA polymerase and its mutants for incorporation of nucleoside analogs into RNA. Methods Enzymol. 317, 65-74. (Pubitemid 30418077)
27. Sousa, R., and Padilla, R. (1995) A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14, 4609-4621.
28. Christian, E. L., and Yarus, M. (1992) Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena. J. Mol. Biol. 228, 743-758. (Pubitemid 23017267)
29. Milligan, J. F., and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51-62. (Pubitemid 20039565)
30. Batey, R. T., Rambo, R. P., Lucast, L., Rha, B., and Doudna, J. A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287, 1232-1239. (Pubitemid 30112139)
31. Beaudry, A. A., and Joyce, G. F. (1992) Directed evolution of an RNA enzyme. Science 257, 635-641.
32. Cech, T. R. (1990) Self-splicing of group I introns. Annu. Rev. Biochem. 59, 543-568.
33. Mei, R., and Herschlag, D. (1996) Mechanistic investigations of a ribozyme derived from the Tetrahymena group I intron: insights into catalysis and the second step of self-splicing. Biochemistry 35, 5796-5809. (Pubitemid 26143675)
34. Lingner, J., and Keller, W. (1993) 3 ¢-End labeling of RNA with recombinant yeast poly(A) polymerase. Nucleic Acids Res. 21, 2917-2920. (Pubitemid 23220445)
35. Ortoleva-Donnelly, L., Szewczak, A. A., Gutell, R. R., and Strobel, S. A. (1998) The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4, 498-519. (Pubitemid 28225419)
36. Soukup, J. K., Minakawa, N., Matsuda, A., and Strobel, S. A. (2002) Identification of A-Minor tertiary interactions within a bacterial group I intron active site by 3-deazaadenosine interference mapping. Biochemistry 41, 10426-10438.
37. Schwans, J. P., Cortez, C. N., Olvera, J. M., and Piccirilli, J. A. (2003) 2 ¢-Mercaptonucleotide interference reveals regions of close packing within folded RNA molecules. J. Am. Chem. Soc. 125, 10012-10018. (Pubitemid 36994930)
38. Strobel, S. A., Ortoleva-Donnelly, L., Ryder, S. P., Cate, J. H., and Moncoeur, E. (1998) Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nat. Struct. Biol. 5, 60-66. (Pubitemid 28048978)
39. Suydam, I. T., and Strobel, S. A. (2008) Fluorine substituted adenosines as probes of nucleobase protonation in functional RNAs. J. Am. Chem. Soc. 130, 13639-13648.
40. Ryder, S. P., Oyelere, A. K., Padilla, J. L., Klostermeier, D., Millar, D. P., and Strobel, S. A. (2001) Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. RNA 7, 1454-1463. (Pubitemid 32973231)
41. Kazantstev, S. V., and Pace, N. R. (1998) Identification by modification-interference of purine N-7 and ribose 2 ¢-OH groups critical for catalysis by bacterial ribonuclease P. RNA 4, 937-947. (Pubitemid 28359764)
42. Ortoleva-Donnelly, L., Kronman, M., and Strobel, S. A. (1998) Identifying RNA minor groove tertiary contacts by nucleotide analog interference mapping with N2-methylguanosine. Biochemistry 37, 12933-12942. (Pubitemid 28433527)
43. Szewczak, A. A., Ortoleva-Donnelly, L., Zivarts, M. V., Oyelere, A. K., Kazantsev, A. V., and Strobel, S. A. (1999) An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proc. Natl. Acad. Sci. U. S. A. 96, 11183-11188. (Pubitemid 29487355)
44. Szewczak, A. A., Ortoleva-Donnelly, L., Ryder, S. P., Moncoeur, E., and Strobel, S. A. (1998) A minor groove RNA triple helix within the catalytic core of a group I intron. Nat. Struct. Biol. 5, 1037-1041.