A chemogenetic approach to RNA function/structure analysis

Current Opinion in Structural Biology

Volumn 9, Issue 3, 1999, Pages 346-352

  Strobel, Scott A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METAL ION; PHOSPHOROTHIOIC ACID; RIBOZYME; RNA;

ANALYTIC METHOD; BINDING SITE; ENZYME MECHANISM; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA BINDING; RNA CONFORMATION; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION;

EID: 0033150681     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)80046-3     Document Type: Article

References (36)

1. Eckstein F: Nucleoside phosphorothioates. Annu Rev Biochem 1985, 54:367-402.
2. Gaur RK, Krupp G: Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme. Nucleic Acids Res 1993, 21:21-26.
3. Strobel SA, Shetty K: Defining the chemical groups essential for tetrahymena group I intron function by nucleotide analog interference mapping. Proc Natl Acad Sci USA 1997, 94:2903-2908. Strobel and Shetty describe interference mapping of the group I intron using the analog inosine and interference suppression using the analog diaminopurine riboside (DAPαS) in the context of a guanine to adenine mutation. This was the first use of base analogs in a NAIM experiment and gives an initial description of interference suppression.
4. Grasby JA, Gait MJ: Synthetic oligoribonucleotides carrying site-specific modifications for RNA structure-function analysis. Biochimie 1994, 76:1223-1234.
5. Griffiths AD, Potter BVL, Eperon IC: Stereospecificity of nucleases towards phosphorothioate-substituted RNA: Stereochemistry of transcription by T7 polymerase. Nucleic Acids Res 1987, 15:4145-4162.
6. Gish G, Eckstein F: DNA and RNA sequence determination based on phosphorothioate chemistry. Science 1988, 240:1520-1522.
7. Christian EL, Yarus M: Metal coordination sites that contribute to structure and catalysis in the group I intron from tetrahymena. Biochemistry 1993, 32:4475-4480.
8. Cate JH, Hanna RL, Doudna JA: A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol 1997, 4:553-558. The structural and biochemical characterization of binding sites for divalent metal ions within the Tetrahymena P4-P6 domain. This work describes a metal ion core at the heart of the RNA domain and provides the best demonstration to date that the sites of phosphorothioate interference correspond to RNA-metal or RNA-RNA interactions.
9. Conrad F, Hanne A, Gaur RK, Krupp G: Enzymatic synthesis of 2′-modified nucleic acids: Identification of important phosphate and ribose moieties in RNase P substrates. Nucleic Acids Res 1995, 23:1845-1853.
10. Ortoleva-Donnelly L, Szewczak AA, Gutell RR, Strobel SA: The chemical basis of adenosine conservation throughout the tetrahymena ribozyme. RNA 1998, 4:498-519.
11. 2-methylguanosine. Biochemistry 1998, 37:12933-12942.
12. + rescue in order to demonstrate that the monovalent metal ion is functionally important.
13. Kazantsev AV, Pace NR: Identification by modification-interference of purine N-7 and ribose 2′-OH groups critical for catalysis by bacterial ribonuclease P. RNA 1998, 4:937-947.
14. 2-methylguanosine is isoenergetic with G in the context of RNA duplexes and GNRA tetraloops. Nucleic Acids Res 1998, 26:3640-3644.
15. Herschlag D, Eckstein F, Cech TR: Contributions of 2′-hydroxyl groups of the RNA substrate to binding and catalysis by the tetrahymena ribozyme. An energetic picture of an active site composed of RNA. Biochemistry 1993, 32:8299-8311.
16. Guschlbauer W, JankowsKi K: Nucleoside conformation is determined by the electronegativity of the sugar substituent. Nucleic Acids Res 1980, 8:1421-1433.
17. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA: Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 1996, 273:1678-1685.
18. p-deoxy-phosphorothioate modification interference experiments identify 2′-OH groups in RNase P RNA that are crucial to tRNA binding. RNA 1996, 2:1189-1198.
19. 2 groups of escherichia coli rnase P RNA involved in intramolecular tertiary contacts and direct interactions with trna. RNA 1999, 5:102-116.
20. Siew D, Zahler NH, Cassano AG, Strobel SA, Harris ME: Identification of adenosine functional groups involved in substrate binding by the ribonuclease P ribozyme. Biochemistry 1999, 38:1873-1883.
21. Boudvillain M, Pyle AM: Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis. EMBO J 1998, 17:7091-7104. The authors used nucleotide analog interference mapping (NAIM) to chemically characterize the group II intron. This paper is noteworthy both for its clever interference selection scheme and for its use of interference suppression in order to identify a new tertiary interaction within the intron.
22. Asp to Its Cognate Synthetase. This Paper Is Particularly Important for The Validation of NAIM because Each Site of 2′ Deoxy Interference Is Confirmed by The ThermodyNamic Characterization of The Single-site Substituted RNA.
23. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA: RNA tertiary structure mediation by adenosine platforms. Science 1996, 273:1696-1699.
24. Strobel SA, Ortoleva-Donnelly L, Ryder SP, Cate JH, Moncoeur E: Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nat Struct Biol 1998, 5:60-66. The use of interference suppression to identify the tertiary hydrogen-bonding interactions that are responsible for 5′ splice site selection in the group I intron. The minor groove of the conserved wobble pair at the cleavage site is complementary to two consecutively stacked, sheared A·A pairs in the ribozyme active site.
25. Szewczak AA, Ortoleva-Donnelly L, Ryder SP, Moncouer E, Strobel SA: A minor groove triple helix in the active site of the tetrahymena group I intron. Nat Struct Biol 1998, 5:1037-1042. The tertiary interactions suggested by interference suppression indicate that the group I active site recognizes its substrate via a minor-groove triple helix. Based upon interference and other constraints, this paper reports a biochemical model of the intron active site that includes a large fraction of the catalytic core.
26. Pyle AM, Cech TR: Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups. Nature 1991, 350:628-631.
27. Bevilacqua PC, Turner DH: Comparison of binding of mixed ribose-deoxyribose analogs of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: Evidence for ribozyme specific interactions with 2′ OH groups. Biochemistry 1991, 30:10632-10640.
28. Strobel SA, Cech TR: Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the tetrahymena ribozyme. Biochemistry 1993, 32:13593-13604.
29. Strobel SA, Cech TR: Minor groove recognition of the conserved G·U pair at the tetrahymena ribozyme reaction site. Science 1995, 267:675-679.
30. Gutell RR, Larsen N, Woese CR: Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 1994, 58:10-26.
31. Gautheret D, Konings D, Gutell RR: A major family of motifs involving G·A mismatches in ribosomal RNA. J Mol Biol 1994, 242:1-8.
32. Pyle AM, Murphy FL, Cech TR: RNA substrate binding site in the catalytic core of the tetrahymena ribozyme. Nature 1992, 358:123-128.
33. Strobel SA, Ortoleva-Donnelly L: A hydrogen bonding triad stabilizes the chemical transition state of a group I ribozyme. Chem Biol 1999, 6:153-165. The characterization of the catalytic mechanism of group I intron splicing using interference suppression. This paper reports that the leaving group of the ribozyme phosphoryl transfer reaction is in part stabilized by a RNA hydrogen-bonding triad.
34. Herschlag D, Eckstein F, Cech TR: The importance of being ribose at the cleavage site in the tetrahymena ribozyme reaction. Biochemistry 1 993, 32:8312-8321.
35. Beese LS, Steitz TA: Structural basis for the 3′-5′ exonuclease activity of escherichia coli DNA polymerase I: A two metal ion mechanism. EMBO J 1991, 10:25-33.
36. Zhang Y, Liang J-Y, Huang S, Ke H, Lipscomb WN: Crystallographic studies of the catalytic mechanism of the neutral form of fructose-1,6-bisphosphatase. Biochemistry 1993, 32:1844-1857.