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Original Articles

Use of Both Direct and Indirect 13C Tags for Probing Nitrogen Interactions in Hairpin Ribozyme Models by 15N NMR

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Pages 273-280 | Received 25 Jul 2003, Accepted 14 Oct 2003, Published online: 01 Jun 2007

References

  • Gaffney , B. L. , Wang , C. and Jones , R. A. 1992 . Nitrogen‐15‐labeled oligodeoxynucleotides. 4. Tetraplex formation of d[G(15N7)GTTTTTGG] and d[T(15N7GGGT] monitored by 1H detected 15N NMR . J. Am. Chem. Soc. , 114 : 4047 – 4050 .
  • Gaffney , B. L. , Goswami , B. and Jones , R. A. 1993 . Nitrogen‐15‐labeled oligodeoxynucleotides. 7. Use of 15N NMR to probe H‐bonding in an O6MeG · C base pair . J. Am. Chem. Soc. , 115 : 12607 – 12608 .
  • Gaffney , B. L. , Kung , P.‐P. , Wang , C. and Jones , R. A. 1995 . Nitrogen‐15‐labeled oligodeoxynucleotides. 8. Use of 15N NMR to probe Hoogsteen hydrogen bonding at guanine and adenine N‐7 atoms of a DNA triplex . J. Am. Chem. Soc. , 117 : 12281 – 12283 .
  • Gao , X. and Jones , R. A. 1987 . Nitrogen‐15‐labeled oligodeoxynucleotides. Characterization by 15N NMR of d[CGTACG] containing 15N1‐ or 15N6‐labeled deoxyadenosine . J. Am. Chem. Soc. , 109 : 3169 – 3171 .
  • Goswami , B. , Gaffney , B. L. and Jones , R. A. 1993 . Nitrogen‐15‐labeled oligodeoxynucleotides. 5. Use of 15N NMR to probe H‐bonding in an O6MeG · T base pair . J. Am. Chem. Soc. , 115 : 3832 – 3833 .
  • Tanaka , Y. , Kojima , C. , Morita , E. H. , Kasai , Y. , Yamasaki , K. , Ono , A. , Kainosho , M. and Taira , K. 2002 . Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using 15N NMR spectroscopy . J. Am. Chem. Soc. , 124 : 4595 – 4601 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Wang , C. , Gao , X. and Jones , R. A. 1991 . Nitrogen‐15‐labeled oligodeoxynucleotides. 2. Solvent isotope effects on the chemical shift of the adenine N1 in an A · T base pair . J. Am. Chem. Soc. , 113 : 1448 – 1450 .
  • Zhang , X. , Gaffney , B. L. and Jones , R. A. 1997 . 15N NMR of a specifically labeled RNA fragment containing intrahelical GU wobble pairs . J. Am. Chem. Soc. , 119 : 6432 – 6433 . [CROSSREF]
  • Zhang , X. , Gaffney , B. L. and Jones , R. A. 1998 . 15N NMR of RNA fragments containing specifically labeled GU and GC pairs . J. Am. Chem. Soc. , 120 : 615 – 618 . [CROSSREF]
  • Zhang , X. , Gaffney , B. L. and Jones , R. A. 1998 . 15N NMR of RNA fragments containing specifically labeled tandem G∑A pairs . J. Am. Chem. Soc. , 120 : 6625 – 6626 . [CROSSREF]
  • Levy , G. C. 1979 . Nitrogen‐15 Nuclear Magnetic Resonance Spectroscopy New York : John Wiley & Sons .
  • Abad , J. L. , Gaffney , B. L. and Jones , R. A. 1999 . 15N‐Multilabeled adenine and guanine nucleosides. Syntheses of [1,3,NH2‐15N3]‐ and [2‐13C‐1,3,NH2‐15N3]‐labeled adenosine, guanosine, 2′‐deoxyadenosine, and 2′‐deoxyguanosine . J. Org. Chem. , 64 : 6575 – 6582 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Pagano , A. R. , Lajewski , W. M. and Jones , R. A. 1995 . Syntheses of [6,7‐15N]‐adenosine, [6,7‐15N]‐2′‐deoxyadenosine, and [7‐15N]‐hypoxanthine . J. Am. Chem. Soc. , 117 : 11669 – 11672 .
  • Pagano , A. R. , Zhao , H. , Shallop , A. and Jones , R. A. 1998 . Syntheses of [1,7‐15N2]‐ and [1,7,NH2‐15N3]‐adenosine and 2′‐deoxyadenosine via an N1‐alkoxy mediated Dimroth rearrangement . J. Org. Chem. , 63 : 3213 – 3217 . [CROSSREF]
  • Shallop , A. J. , Gaffney , B. L. and Jones , R. A. 2003 . Use of 13C as an indirect tag in 15N specifically labeled nucleosides. Syntheses of [8‐13C‐1,7,NH2‐15N3]‐adenosine, ‐guanosine, and their deoxy analogs . J. Org. Chem. , 68 : 8657 – 8661 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Zhao , H. , Pagano , A. R. , Wang , W. , Shallop , A. , Gaffney , B. L. and Jones , R. A. 1997 . Use of a 13C atom to differentiate two 15N‐labeled nucleosides. Syntheses of [6‐15N]‐adenosine; [1,2‐15N]‐ and [1,2‐15N‐2‐13C]‐guanosines; [1,2,7‐15N]‐ and [1,2,7‐15N‐2‐13C]‐2′deoxyguanosine . J. Org. Chem. , 62 : 7832 – 7835 . [CROSSREF]
  • Hampel , A. , Tritz , R. , Hicks , M. and Cruz , P. 1990 . Hairpin catalytic RNA model, evidence for helices and sequence requirement for substrate RNA . Nucleic Acids Res. , 18 : 299 – 304 . [PUBMED] [INFOTRIEVE]
  • Long , D. M. and Uhlenbeck , O. C. 1993 . Self‐cleaving catalytic RNA . FASEB J. , 7 : 25 – 30 . [PUBMED] [INFOTRIEVE] [CSA]
  • Symons , R. H. 1992 . Small catalytic RNAs . Ann. Rev. Biochem. , 61 : 641 – 671 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
  • Walter , N. G. and Burke , J. M. 1998 . The hairpin ribozyme: structure, assembly and catalysis . Curr. Opin. Struct. Biol. , 2 : 24 – 30 .
  • Nesbitt , S. , Hegg , L. A. and Fedor , M. J. 1997 . An unusual pH‐independent and metal‐ion‐independent mechanism for hairpin ribozyme catalysis . Chem. Biol. , 4 : 619 – 630 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
  • Young , K. J. , Gill , F. and Grasby , J. A. 1997 . Metal ions play a passive role in the hairpin ribozyme catalysed reaction . Nucleic Acids Res. , 25 : 3760 – 3766 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Butcher , S. E. , Allain , F. H.‐T. and Feigon , J. 1999 . Solution structure of the loop B domain from the hairpin ribozyme . Nat. Struct. Biol. , 6 : 212 – 216 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
  • Cai , Z. and Tinoco , I. Jr. 1996 . Solution structure of Loop A from the hairpin ribozyme from tobacco ringspot virus satellite . Biochemistry , 35 : 6026 – 6036 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Rupert , P. B. and Ferre‐D'Amare , A. R. 2001 . Crystal structure of a hairpin ribozyme‐inhibitor complex with implications for catalysis . Nature (Lond.) , 410 : 780 – 786 . [CROSSREF]
  • Rupert , P. B. , Massey , A. P. , Sigurdsson , S. T. and Ferre‐D'Amare , A. R. 2002 . Transition state stabilization by a catalytic RNA . Science , 298 : 1421 – 1424 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Pinard , R. , Hampel , K. J. , Heckmean , J. E. , Lambert , D. , Chan , P. A. , Major , F. and Burke , J. M. 2001 . Functional involvement of G8 in the hairpin ribozyme cleavege mechanism . EMBO J. , 20 : 6434 – 6442 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
  • Saenger , W. 1984 . Principles of Nucleic Acid Structure New York : Springer‐Verlag .
  • Connell , G. J. and Yarus , M. 1994 . RNAs with dual specificity and dual RNAs with similar specificity . Science , 264 : 1137 – 1141 . [PUBMED] [INFOTRIEVE]
  • Legault , P. and Pardi , A. 1997 . Unusual dynamics and pKa shift at the active site of a lead‐dependent ribozyme . J. Am. Chem. Soc. , 119 : 6621 – 6628 . [CROSSREF]
  • Muth , G. W. , Ortoleva‐Donnelly , L. and Strobel , S. A. 2000 . A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center . Science , 289 : 947 – 950 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Nakano , S.‐i. , Chadalavada , D. M. and Bevilacqua , P. C. 2000 . General acid‐base catalysis in the mechanism of a hepatitis delta virus ribozyme . Science , 287 : 1493 – 1497 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Ravindranathan , S. , Butcher , S. E. and Feigon , J. 2000 . Adenine protonation in domain B of the hairpin ribozyme . Biochemistry , 39 : 16026 – 16032 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Büchner , P. , Maurer , W. and Rüterjans , H. 1978 . Nitrogen‐15 nuclear magnetic resonance spectroscopy of 15N‐labeled nucleotides . J. Magn. Reson. , 29 : 45 – 63 .
  • Butcher , S. E. , Allain , F. H.‐T. and Feigon , J. 2000 . Determination of metal binding sites within the hairpin ribozyme domains by NMR . Biochemistry , 39 : 2174 – 2182 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Buchanan , G. W. 1989 . Applications of 15N NMR spectroscopy to the study of molecular structure, stereochemistry and binding phenemena . Tetrahedron , 45 : 581 – 604 . [CROSSREF]
  • Song , Q. , Wang , W. , Fischer , A. , Zhang , X. , Gaffney , B. L. and Jones , R. A. 1999 . High yield protection of purine ribonucleosides for phosphoramidite RNA synthesis . Tetrahedron Lett. , 40 : 4153 – 4156 . [CROSSREF]
  • Nielsen , J. , Taagaard , M. , Marugg , J. E. , Boom , J. H.v. and Dahl , O. 1986 . Application of 2‐cyanoethyl N,N,N′,N′‐tetraisopropylphosphorodiamidite for in situ preparation of deoxyribonucleoside phosphoramidites and their use in polymer‐supported synthesis of oligodeoxyribonucleotides . Nucleic Acids Res. , 14 : 7391 – 7403 . [PUBMED] [INFOTRIEVE]
  • Sanghvi , Y. S. , Guo , Z. , Pfundheller , H. M. and Converso , A. 2000 . Improved process for the preparation of nucleosidic phosphoramidites using a safer and cheaper activator . Org. Process Res. Dev. , 4 : 175 – 181 . [CROSSREF]
  • Vargeese , C. , Carter , J. , Yegge , J. , Krivjansky , S. , Settle , A. , Kropp , E. , Peterson , K. and Pieken , W. 1998 . Efficient activation of nucleoside phosphoramidites with 4,5‐dicyanoimidazole during oligonucleotide synthesis . Nucleic Acids Res. , 26 : 1046 – 1050 . [PUBMED] [INFOTRIEVE] [CROSSREF]
  • Wincott , F. , DeRenzo , A. , Shaffer , C. , Grimm , S. , Tracz , D. , Workman , C. , Sweedler , D. , Gonzalez , C. , Scaringe , S. and Usman , N. 1995 . Synthesis, deprotection, analysis and purification of RNA and ribozymes . Nucleic Acids Res. , 23 : 2677 – 2684 . [PUBMED] [INFOTRIEVE]
  • Song , Q. and Jones , R. A. 1999 . Use of silyl ethers as fluoride scavengers in RNA synthesis . Tetrahedron Lett. , 40 : 4653 – 4654 . [CROSSREF]
  • Wishart , D. S. , Bigam , C. G. , Yao , J. , Abildgaard , F. , Dyson , H. J. , Oldfield , E. , Markley , J. L. and Sykes , B. D. 1995 . 1H, 13C and 15N chemical shift referencing in biomolecular NMR . J. Biomol. NMR , 6 : 135 – 140 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]

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