2′-Fluoro substituents can mimic native 2′-hydroxyls within structured RNA

Chemistry and Biology

Volumn 18, Issue 8, 2011, Pages 949-954

  Forconi, Marcello ^a,b   Schwans, Jason P ^a,c   Porecha, Rishi H ^a   Sengupta, Raghuvir N ^a,c   Piccirilli, Joseph A ^b,c   Herschlag, Daniel ^a  

^a STANFORD UNIVERSITY   (United States)

^b School of Business   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TETRAHYMENA;

FLUORINE; GIR1 RIBOZYME; HYDROXYL RADICAL; PURINE; PURINE DERIVATIVE; RIBOZYME; RNA;

ARTICLE; CHEMISTRY; CONFORMATION; HYDROGEN BOND; TETRAHYMENA;

FLUORINE; HYDROGEN BONDING; HYDROXYL RADICAL; NUCLEIC ACID CONFORMATION; PURINES; RNA; RNA, CATALYTIC; TETRAHYMENA;

EID: 80052158929     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2011.07.014     Document Type: Article

References (52)

1. S. Basu, and S.A. Strobel Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain RNA 5 1999 1399 1407 (Pubitemid 29530484)
2. D.J. Battle, and J.A. Doudna Specificity of RNA-RNA helix recognition Proc. Natl. Acad. Sci. USA 99 2002 11676 11681 (Pubitemid 34994458)
3. P.C. Bevilacqua, and D.H. Turner 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 1991 10632 10640
4. E. Carosati, S. Sciabola, and G. Cruciani Hydrogen bonding interactions of covalently bonded fluorine atoms: from crystallographic data to a new angular function in the GRID force field J. Med. Chem. 47 2004 5114 5125 (Pubitemid 39314909)
5. J.H. Cate, A.R. Gooding, E. Podell, K. Zhou, B.L. Golden, C.E. Kundrot, T.R. Cech, and J.A. Doudna Crystal structure of a group I ribozyme domain: principles of RNA packing Science 273 1996 1678 1685 (Pubitemid 26317777)
6. C. Chatterjee, and T.W. Muir Chemical approaches for studying histone modifications J. Biol. Chem. 285 2010 11045 11050
7. S.R. Das, R. Fong, and J.A. Piccirilli Nucleotide analogues to investigate RNA structure and function Curr. Opin. Chem. Biol. 9 2005 585 593 (Pubitemid 41613882)
8. J.D. Dunitz Organic fluorine: odd man out ChemBioChem 5 2004 614 621 (Pubitemid 39257082)
9. J.D. Dunitz, and R. Taylor Organic fluorine hardly ever accepts hydrogen bonds Chem. Eur. J. 3 1997 89 98 (Pubitemid 27185111)
10. M. Forconi, R.N. Sengupta, M.C. Liu, A.C. Sartorelli, J.A. Piccirilli, and D. Herschlag Structure and function converge to identify a hydrogen bond in a group I ribozyme active site Angew. Chem. Int. Ed. Engl. 48 2009 7171 7175
11. M. Forconi, R.N. Sengupta, J.A. Piccirilli, and D. Herschlag A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site Biochemistry 49 2010 2753 2762
12. M. Forconi, R.H. Porecha, J.A. Piccirilli, and D. Herschlag Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme J. Am. Chem. Soc. 133 2011 7791 7800
13. B.L. Golden, H. Kim, and E. Chase Crystal structure of a phage Twort group I ribozyme-product complex Nat. Struct. Mol. Biol. 12 2005 82 89 (Pubitemid 40082921)
14. W. Guschlbauer, and K. Jankowski Nucleoside conformation is determined by the electronegativity of the sugar substituent Nucleic Acids Res. 8 1980 1421 1433
15. M.E. Hahn, and T.W. Muir Manipulating proteins with chemistry: a cross-section of chemical biology Trends Biochem. Sci. 30 2005 26 34 (Pubitemid 40093738)
16. D. Herschlag Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme Biochemistry 31 1992 1386 1399
17. J.L. Hougland, A.V. Kravchuk, D. Herschlag, and J.A. Piccirilli Functional identification of catalytic metal ion binding sites within RNA PLoS Biol. 3 2005 1536 1548 (Pubitemid 41306437)
18. J.L. Hougland, J.A. Piccirilli, M. Forconi, J. Lee, and D. Herschlag How the group I intron works: A case study of RNA structure and function R.F. Gesteland, T.R. Cech, J.F. Atkins, The RNA World 2006 Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York 133 205
19. J.A.K. Howard, V.J. Hoy, D. O'Hagan, and G.T. Smith How good is fluorine as a hydrogen bond acceptor? Tetrahedron 52 1996 12613 12622 (Pubitemid 26295489)
20. K. Juneau, E. Podell, D.J. Harrington, and T.R. Cech Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA - solvent interactions Structure 9 2001 221 231 (Pubitemid 32245873)
21. A.M. Kawasaki, M.D. Casper, S.M. Freier, E.A. Lesnik, M.C. Zounes, L.L. Cummins, C. Gonzalez, and P.D. Cook Uniformly modified 2′-deoxy-2′- fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets J. Med. Chem. 36 1993 831 841 (Pubitemid 23118776)
22. S.V. Lipchock, and S.A. Strobel A relaxed active site after exon ligation by the group I intron Proc. Natl. Acad. Sci. USA 105 2008 5699 5704 (Pubitemid 351758435)
23. J.L. Martin, L.N. Johnson, and S.G. Withers Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b Biochemistry 29 1990 10745 10757
24. S. Matsumura, Y. Ikawa, and T. Inoue Biochemical characterization of the kink-turn RNA motif Nucleic Acids Res. 31 2003 5544 5551 (Pubitemid 37441924)
25. J.D. McCarter, M.J. Adam, and S.G. Withers Binding energy and catalysis. Fluorinated and deoxygenated glycosides as mechanistic probes of Escherichia coli (lacZ) beta-galactosidase Biochem. J. 286 1992 721 727
26. G. Mehta, and S. Sen Probing fluorine interactions in a polyhydroxylated environment: conservation of a C-F·····H-C recognition motif in presence of O-H·····O hydrogen bonds Eur. J. Org. Chem. 2010 3387-3394
27. M.J. Moore, and P.A. Sharp Site-specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites Science 256 1992 992 997
28. S. Moran, R. Kierzek, and D.H. Turner Binding of guanosine and 3′ splice site analogues to a group I ribozyme: interactions with functional groups of guanosine and with additional nucleotides Biochemistry 32 1993 5247 5256 (Pubitemid 23162095)
29. K. Müller, C. Faeh, and F. Diederich Fluorine in pharmaceuticals: looking beyond intuition Science 317 2007 1881 1886 (Pubitemid 47509426)
30. F.L. Murphy, Y.H. Wang, J.D. Griffith, and T.R. Cech Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme Science 265 1994 1709 1712 (Pubitemid 24314902)
31. P. Murray-Rust, W.C. Stallings, C.T. Monti, R.K. Preston, and J.P. Glusker Intermolecular interactions of the carbon-fluorine bond: the crystallographic environment of fluorinated carboxylic-acids and related structures J. Am. Chem. Soc. 105 1983 3206 3214
32. M.N. Namchuk, and S.G. Withers Mechanism of Agrobacterium beta-glucosidase: kinetic analysis of the role of noncovalent enzyme/substrate interactions Biochemistry 34 1995 16194 16202 (Pubitemid 3013249)
33. W.A. Offen, D.L. Zechel, S.G. Withers, H.J. Gilbert, and G.J. Davies Structure of the Michaelis complex of beta-mannosidase, Man2A, provides insight into the conformational itinerary of mannoside hydrolysis Chem. Commun. (Camb) 2009 2484 2486
34. D. O'Hagan, and H.S. Rzepa Some influences of fluorine in bioorganic chemistry Chem. Commun. (Camb) 1997 645 652 (Pubitemid 127498767)
35. L. Ortoleva-Donnelly, A.A. Szewczak, R.R. Gutell, and S.A. Strobel The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme RNA 4 1998 498 519 (Pubitemid 28225419)
36. L. Pauling The nature of chemical bonds. IV. The energy of single bonds and the relative electronegativity of atoms J. Am. Chem. Soc. 54 1932 3570 3582
37. M.D. Percival, and S.G. Withers Binding energy and catalysis: deoxyfluoro sugars as probes of hydrogen bonding in phosphoglucomutase Biochemistry 31 1992 498 505
38. K. Persson, H.D. Ly, M. Dieckelmann, W.W. Wakarchuk, S.G. Withers, and N.C. Strynadka Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs Nat. Struct. Biol. 8 2001 166 175 (Pubitemid 32116071)
39. R. Russell, and D. Herschlag Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme RNA 5 1999 158 166 (Pubitemid 29079276)
40. S.P. Ryder, L. Ortoleva-Donnelly, A.B. Kosek, and S.A. Strobel Chemical probing of RNA by nucleotide analog interference mapping Methods Enzymol. 317 2000 92 109 (Pubitemid 30418079)
41. S.P. Ryder, and S.A. Strobel Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation J. Mol. Biol. 291 1999 295 311 (Pubitemid 29381429)
42. B.D. Sattin, W. Zhao, K. Travers, S. Chu, and D. Herschlag Direct measurement of tertiary contact cooperativity in RNA folding J. Am. Chem. Soc. 130 2008 6085 6087 (Pubitemid 351657284)
43. J.C. Schlatterer, L.W. Kwok, J.S. Lamb, H.Y. Park, K. Andresen, M. Brenowitz, and L. Pollack Hinge stiffness is a barrier to RNA folding J. Mol. Biol. 379 2008 859 870
44. J.P. Schwans, C.N. Cortez, J.M. Olvera, and J.A. Piccirilli 2′-mercaptonucleotide interference reveals regions of close packing within folded RNA molecules J. Am. Chem. Soc. 125 2003 10012 10018 (Pubitemid 36994930)
45. J.P. Schwans, N.S. Li, and J.A. Piccirilli A packing-density metric for exploring the interior of folded RNA molecules Angew. Chem. Int. Ed. Engl. 43 2004 3033 3037 (Pubitemid 39257624)
46. M.R. Stahley, and S.A. Strobel Structural evidence for a two-metal-ion mechanism of group I intron splicing Science 309 2005 1587 1590 (Pubitemid 41266489)
47. I.P. Street, C.R. Armstrong, and S.G. Withers Hydrogen bonding and specificity. Fluorodeoxy sugars as probes of hydrogen bonding in the glycogen phosphorylase-glucose complex Biochemistry 25 1986 6021 6027 (Pubitemid 17204036)
48. I.P. Street, K. Rupitz, and S.G. Withers Fluorinated and deoxygenated substrates as probes of transition-state structure in glycogen phosphorylase Biochemistry 28 1989 1581 1587 (Pubitemid 19072028)
49. K. Takamoto, R. Das, Q. He, S. Doniach, M. Brenowitz, D. Herschlag, and M.R. Chance Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations J. Mol. Biol. 343 2004 1195 1206 (Pubitemid 39387820)
50. J. Wicki, J. Schloegl, C.A. Tarling, and S.G. Withers Recruitment of both uniform and differential binding energy in enzymatic catalysis: xylanases from families 10 and 11 Biochemistry 46 2007 6996 7005 (Pubitemid 46906428)
51. J.D. Ye, V. Tereshko, J.K. Frederiksen, A. Koide, F.A. Fellouse, S.S. Sidhu, S. Koide, A.A. Kossiakoff, and J.A. Piccirilli Synthetic antibodies for specific recognition and crystallization of structured RNA Proc. Natl. Acad. Sci. USA 105 2008 82 87
52. B.T. Young, and S.K. Silverman The GAAA tetraloop-receptor interaction contributes differentially to folding thermodynamics and kinetics for the P4-P6 RNA domain Biochemistry 41 2002 12271 12276