A role for hydrophobicity in a Diels-Alder reaction catalyzed by pyridyl-modified RNA

Nucleic Acids Research

Volumn 37, Issue 9, 2009, Pages 3074-3082

  Gagnon, Keith T ^a   Ju, Show Yi ^a   Goshe, Michael B ^a   Maxwell, E Stuart ^a   Franzen, Stefan ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTHRACENE DERIVATIVE; COPPER ION; MALEIMIDE DERIVATIVE; PYRIDYL MODIFIED RNA; RNA; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CHEMICAL MODIFICATION; CONTROLLED STUDY; CYCLOADDITION; DIELS ALDER REACTION; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; REACTION ANALYSIS; RNA SEQUENCE; RNA STRUCTURE;

ANTHRACENES; BASE SEQUENCE; CATALYSIS; ETHYLENE GLYCOLS; HYDROPHOBICITY; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PYRIDINES; RNA; RNA, CATALYTIC;

ALNUS;

EID: 66249138832     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp177     Document Type: Article

References (56)

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. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. and Altman, S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35, 849-857.
3. Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
4. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment - RNA ligands to bacteriophage-T4 DNA-polymerase. Science, 249, 505-510.
5. Stoltenburg, R., Reinemann, C. and Strehlitz, B. (2007) SELEX-A (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng., 24, 381-403.
6. Seelig, B. and Jaschke, A. (1999) A small catalytic RNA motif with Diels-Alderase activity. Chem. Biol., 6, 167-176.
7. Chandra, M. and Silverman, S.K. (2008) DNA and RNA can be equally efficient catalysts for carbon-carbon bond formation. J. Am. Chem. Soc., 130, 2936-2937.
8. Stahley, M.R. and Strobel, S.A. (2006) RNA splicing: Group I intron crystal structures reveal the basis of splice site selection and metal ion catalysis. Curr. Opin. Struct. Biol., 16, 319-326.
9. Lehmann, K. and Schmidt, U. (2003) Group II introns: Structure and catalytic versatility of large natural ribozymes. Crit. Rev. Biochem. Mol. Biol., 38, 249-303.
10. Ban, N., Nissen, P., Hansen, J., Moore, P.B. and Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution. Science, 289, 905-920.
11. Scott, W.G., Finch, J.T. and Klug, A. (1995) The crystal-structure of an all-RNA hammerhead ribozyme - a proposed mechanism for RNA catalytic cleavage. Cell, 81, 991-1002.
12. Marquez, S.M., Chen, J.L., Evans, D. and Pace, N.R. (2006) Structure and function of eukaryotic ribonuclease P RNA. Mol. Cell, 24, 445-456.
13. Valadkhan, S. and Manley, J.L. (2001) Splicing-related catalysis by protein-free snRNAs. Nature, 413, 701-707.
14. Breaker, R.R. (1997) DNA enzymes. Nat. Biotechnol., 15, 427-431.
15. Narlikar, G.J. and Herschlag, D. (1997) Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes. Ann. Rev. Biochem., 66, 19-59.
16. Battersby, T.R., Ang, D.N., Burgstaller, P., Jurczyk, S.C., Bowser, M.T., Buchanan, D.D., Kennedy, R.T. and Benner, S.A. (1999) Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog. J. Am. Chem. Soc., 121, 9781-9789.
17. Keefe, A.D. and Cload, S.T. (2008) SELEX with modified nucleotides. Curr. Opin. Chem. Biol., 12, 448-456.
18. Latham, J.A., Johnson, R. and Toole, J.J. (1994) The application of a modified nucleotide in aptamer selection - novel thrombin aptamers containing 5-(1-pentynyl)-2′-deoxyuridine. Nucleic Acids Res., 22, 2817-2822.
19. Perrin, D.M., Garestier, T. and Helene, C. (2001) Bridging the gap between proteins and nucleic acids: A metal-independent RNAseA mimic with two protein-like functionalities. J. Am. Chem. Soc., 123 1556-1563.
20. Santoro, S.W., Joyce, G.F., Sakthivel, K., Gramatikova, S. and Barbas, C.F. (2000) RNA cleavage by a DNA enzyme with extended chemical functionality. J. Am. Chem. Soc., 122, 2433-2439.
21. Tarasow, T.M., Tarasow, S.L. and Eaton, B.E. (1997) RNA-catalysed carbon-carbon bond formation. Nature, 389, 54-57.
22. Vaish, N.K., Larralde, R., Fraley, A.W., Szostak, J.W. and McLaughlin, L.W. (2003) A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality. Biochemistry, 42, 8842-8851.
23. Ting, R., Thomas, J.M., Lermer, L. and Perrin, D.M. (2004) Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: A putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation. Nucleic Acids Res., 32 6660-6672.
24. 2+). Nucleic Acids Res., Advance Access published on January 19, 2009; doi: 10.1093/nar/gkn1070.
25. Nicolaou, K.C., Snyder, S.A., Montagnon, T. and Vassilikogiannakis, G. (2002) The Diels-Alder reaction in total synthesis. Angew. Chem. Intl. Ed., 41, 1668-1698.
26. Corey, E.J. and Cheng, X.-M. (1989) The Logic of Chemical Synthesis Wiley, New York, NY.
27. Morris, K.N., Tarasow, T.M., Julin, C.M., Simons, S.L., Hilvert, D. and Gold, L. (1994) Enrichment for RNA molecules that bind a Diels-Alder transition-state analog. Proc. Natl Acad. Sci. USA, 91, 13028-13032.
28. Tarasow, T.M., Kellogg, E., Holley, B.L., Nieuwlandt, D., Tarasow, S.L. and Eaton, B.E. (2004) The effect of mutation on RNA Diels-Alderases. J. Am. Chem. Soc., 126, 11843-11851.
29. Seelig, B., Keiper, S., Stuhlmann, F. and Jaschke, A. (2000) Enantioselective ribozyme catalysis of a bimolecular cycloaddition reaction. Angew. Chem.-Intl. Ed., 39, 4576-4579.
30. Keiper, S., Bebenroth, D., Seelig, B., Westhof, E. and Jaschke, A. (2004) Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket. Chem. Biol., 11, 1217-1227.
31. Serganov, A., Keiper, S., Malinina, L., Tereshko, V., Skripkin, E., Hobartner, C., Polonskaia, A., Phan, A.T., Wombacher, R., Micura, R. et al. (2005) Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat. Struct. Mol. Biol., 12, 218-224.
32. Chiorcea-Paquim, A.M., Piedade, J.A.P., Wombacher, R., Jaschke, A. and Oliveira-Brett, A.M. (2006) Atomic force microscopy and anodic voltammetry characterization of a 49-mer Diels-Alderase ribozyme. Anal. Chem., 78, 8256-8264.
33. 2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis. Nucleic Acids Res., 35, 2047-2059.
34. Wombacher, R., and Jaschke, A. (2008) Probing the active site of a Diels-Alderase ribozyme by photoaffinity cross-linking. J. Am. Chem. Soc., 130, 8594-8595.
35. Heine, A., Stura, E.A., Yli-Kauhaluoma, J.T., Gao, C.S., Deng, Q.L., Beno, B.R., Houk, K.N., Janda, K.D. and Wilson, I.A. (1998) An antibody exo Diels-Alderase inhibitor complex at 1.95 angstrom resolution. Science, 279, 1934-1940.
36. Romesberg, F.E., Spiller, B., Schultz, P.G. and Stevens, R.C. (1998) Immunological origins of binding and catalysis in a Diels-Alderase antibody. Science, 279, 1929-1933.
37. Hugot, M., Bensel, N., Vogel, M., Reymond, M.T., Stadler, B., Reymond, J.L. and Baumann, U. (2002) A structural basis for the activity of retro-Diels-Alder catalytic antibodies: Evidence for a catalytic aromatic residue. Proc. Natl Acad. Sci. USA, 99. 9674-9678.
38. Breslow, R. (1991) How do imidazole groups catalyze the cleavage of RNA in enzyme models and in enzymes - evidence from negative catalysis. Acc. Chem. Res., 24, 317-324.
39. Tarasow, T.M., Tarasow, S.L. and Eaton, B.E. (2000) RNA Diels-Alderases: relationships between unique sequences and catalytic function. J. Am. Chem. Soc., 122, 1015-1021.
40. Tarasow, T.M., Tarasow, S.L., Tu, C., Kellogg, E. and Eaton, B.E. (1999) Characteristics of an RNA Diels-Alderase active site. J. Am. Chem. Soc., 121, 3614-3617.
41. Gagnon, K.T., Zhang, X.X., Agris, P.F. and Maxwell, E.S. (2006) Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling. J. Mol. Biol., 362, 1025-1042.
42. Bhattacharya, S. and Mandal, S.S. (1997) Interaction of surfactants with DNA. Role of hydrophobicity and surface charge on intercalation and DNA melting. Biochim. Biophys. Acta. Biomem., 1323, 29-44.
43. Tan, W.B., Bhambhani, A., Duff, M.R., Rodger, A. and Kumar, C.V. (2006) Spectroscopic identification of binding modes of anthracene probes and DNA sequence recognition. Photochem. Photobiol., 82, 20-30.
44. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
45. Tran, E.J., Zhang, X.X. and Maxwell, E.S. (2003) Efficient RNA 2′-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C0/D0 RNPs. EMBO J., 22, 3930-3940.
46. Hofacker, I.L., Fekete, M. and Stadler, P.F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
47. Batey, R.T., Gilbert, S.D. and Montange, R.K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415.
48. Rideout, D.C. and Breslow, R. (1980) Hydrophobic acceleration of Diels-Alder reactions. J. Am. Chem. Soc., 102, 7816-7817.
49. Otto, S. and Engberts, J. (1999) A systematic study of ligand effects on a Lewis-acid-catalyzed Diels-Alder reaction in water. Water-enhanced enantioselectivity. J. Am. Chem. Soc., 121, 6798-6806.
50. Boersma, A.J., Klijn, J.E., Feringa, B.L. and Roelfes, G. (2008) DNA-based asymmetric catalysis: Sequence-dependent rate acceleration and enantioselectivity. J. Am. Chem. Soc., 130, 11783-11790.
51. Roelfes, G., Boersma, A.J. and Feringa, B.L. (2006) Highly enantioselective DNA-based catalysis. Chem. Commun., 635-637
52. Limbach, P.A., Crain, P.F. and McCloskey, J.A. (1994) Summary: The modified nucleosides of RNA. Nucleic Acids Res., 22, 2183-2196.
53. Xu, L.H., Fushinobu, S., Ikeda, H., Wakagi, T. and Shoun, H. (2009) Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: Conformational flexibility and histidine ligation state. J. Bacteriol., 191, 1211-1219.
54. Ekins, S. (2004) Predicting undesirable drug interactions with promiscuous proteins in silico. Drug Discov. Today, 9, 276-285.
55. Adams, J.D., Yagi, H., Levin, W. and Jerina, D.M. (1995) Stereoselectivity and regioselectivity in the metabolism of 7, 8-dihydrobenzo[a]pyrene by cytochrome-P450, epoxide hydrolase and hepatic microsomes from 3-methylcholanthrene-treated rats. Chem. Biol. Interact., 95, 57-77.
56. Boyd, G.W., Young, R.J., Harvey, R.G., Coombs, M.M. and Ioannides, C. (1993) The metabolism and activation of 15, 16-dihy-drocyclopenta [a]phenanthren-17-one by cytochrome-P-450 proteins. Eur. J. Pharmacol. Env. Tox. Pharm. Sect., 228, 275-282.