메뉴 건너뛰기




Volumn , Issue , 2013, Pages 135-167

An integrated picture of HDV ribozyme catalysis

Author keywords

Molecular dynamics; Raman spectroscopy; Ribozyme; RNA catalysis; RNA folding; X ray crystallography

Indexed keywords


EID: 85027554708     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-4954-6_8     Document Type: Chapter
Times cited : (12)

References (92)
  • 1
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA (2004) Crystal structure of a self-splicing group I intron with both exons. Nature 430(6995):45-50.
    • (2004) Nature , vol.430 , Issue.6995 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Kosek, A.B.3    Wang, J.4    Strobel, S.A.5
  • 3
    • 4344584210 scopus 로고    scopus 로고
    • Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength
    • Brown TS, Chadalavada DM, Bevilacqua PC (2004) Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. J Mol Biol 341(3):695-712. doi:10.1016/j.jmb.2004.05.071.
    • (2004) J Mol Biol , vol.341 , Issue.3 , pp. 695-712
    • Brown, T.S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 5
    • 33646727439 scopus 로고    scopus 로고
    • Raman crystallography and other biochemical applications of raman microscopy
    • Carey PR (2006) Raman crystallography and other biochemical applications of raman microscopy. Ann Rev Phys Chem 57:527-554.
    • (2006) Ann Rev Phys Chem , vol.57 , pp. 527-554
    • Carey, P.R.1
  • 6
    • 50649109849 scopus 로고    scopus 로고
    • Mechanistic characterization of the HDV genomic ribozyme: The cleavage site base pair plays a structural role in facilitating catalysis
    • Cerrone-Szakal AL, Chadalavada DM, Golden BL, Bevilacqua PC (2008) Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis. RNA 14(9):1746-1760. doi:10.1261/rna.1140308.
    • (2008) RNA , vol.14 , Issue.9 , pp. 1746-1760
    • Cerrone-szakal, A.L.1    Chadalavada, D.M.2    Golden, B.L.3    Bevilacqua, P.C.4
  • 7
    • 36248964100 scopus 로고    scopus 로고
    • Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions
    • Chadalavada DM, Cerrone-Szakal AL, Bevilacqua PC (2007) Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions. RNA 13(12):2189-2201. doi:10.1261/ rna.778107.
    • (2007) RNA , vol.13 , Issue.12 , pp. 2189-2201
    • Chadalavada, D.M.1    Cerrone-szakal, A.L.2    Bevilacqua, P.C.3
  • 8
    • 77953894191 scopus 로고    scopus 로고
    • The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting
    • Chadalavada DM, Gratton EA, Bevilacqua PC (2010) The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting. Biochemistry 49(25):5321-5330. doi:10.1021/bi100434c.
    • (2010) Biochemistry , vol.49 , Issue.25 , pp. 5321-5330
    • Chadalavada, D.M.1    Gratton, E.A.2    Bevilacqua, P.C.3
  • 9
    • 0034636981 scopus 로고    scopus 로고
    • A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme
    • Chadalavada DM, Knudsen SM, Nakano S, Bevilacqua PC (2000) A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. J Mol Biol 301(2):349-367. doi:10.1006/jmbi.2000.3953.
    • (2000) J Mol Biol , vol.301 , Issue.2 , pp. 349-367
    • Chadalavada, D.M.1    Knudsen, S.M.2    Nakano, S.3    Bevilacqua, P.C.4
  • 10
    • 0036289258 scopus 로고    scopus 로고
    • The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots
    • Chadalavada DM, Senchak SE, Bevilacqua PC (2002) The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J Mol Biol 317(4):559-575. doi:10.1006/jmbi.2002.5434.
    • (2002) J Mol Biol , vol.317 , Issue.4 , pp. 559-575
    • Chadalavada, D.M.1    Senchak, S.E.2    Bevilacqua, P.C.3
  • 11
    • 61749093844 scopus 로고    scopus 로고
    • A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme
    • Chen JH, Gong B, Bevilacqua PC, Carey PR, Golden BL (2009) A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme. Biochemistry 48(7):1498-1507. doi:10.1021/bi8020108.
    • (2009) Biochemistry , vol.48 , Issue.7 , pp. 1498-1507
    • Chen, J.H.1    Gong, B.2    Bevilacqua, P.C.3    Carey, P.R.4    Golden, B.L.5
  • 12
    • 77955258795 scopus 로고    scopus 로고
    • A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
    • Chen JH, Yajima R, Chadalavada DM, Chase E, Bevilacqua PC, Golden BL (2010) A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. Biochemistry 49(31):6508-6518. doi:10.1021/ bi100670p.
    • (2010) Biochemistry , vol.49 , Issue.31 , pp. 6508-6518
    • Chen, J.H.1    Yajima, R.2    Chadalavada, D.M.3    Chase, E.4    Bevilacqua, P.C.5    Golden, B.L.6
  • 13
    • 77950412602 scopus 로고    scopus 로고
    • A quantitative Raman spectroscopic signal for metal-phosphodiester interactions in solution
    • Christian EL, Anderson VE, Carey PR, Harris ME (2010) A quantitative Raman spectroscopic signal for metal-phosphodiester interactions in solution. Biochemistry 49(13):2869-2879. doi:10.1021/bi901866u.
    • (2010) Biochemistry , vol.49 , Issue.13 , pp. 2869-2879
    • Christian, E.L.1    Anderson, V.E.2    Carey, P.R.3    Harris, M.E.4
  • 14
    • 33846279049 scopus 로고    scopus 로고
    • Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor
    • Cochrane JC, Lipchock SV, Strobel SA (2007) Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor. Chem Biol 14(1):97-105. doi:10.1016/j.chembiol.2006.12.005.
    • (2007) Chem Biol , vol.14 , Issue.1 , pp. 97-105
    • Cochrane, J.C.1    Lipchock, S.V.2    Strobel, S.A.3
  • 15
    • 0035020626 scopus 로고    scopus 로고
    • The hammerhead cleavage reaction in monovalent cations
    • Curtis EA, Bartel DP (2001) The hammerhead cleavage reaction in monovalent cations. RNA 7(4):546-552.
    • (2001) RNA , vol.7 , Issue.4 , pp. 546-552
    • Curtis, E.A.1    Bartel, D.P.2
  • 16
    • 24644454458 scopus 로고    scopus 로고
    • General acid catalysis by the hepatitis delta virus ribozyme
    • Das SR, Piccirilli JA (2005) General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol 1(1):45-52. doi:10.1038/nchembio703.
    • (2005) Nat Chem Biol , vol.1 , Issue.1 , pp. 45-52
    • Das, S.R.1    Piccirilli, J.A.2
  • 17
    • 0038170015 scopus 로고    scopus 로고
    • Metal ion binding to catalytic RNA molecules
    • DeRose VJ (2003) Metal ion binding to catalytic RNA molecules. Curr Opin Struct Biol 13(3):317-324.
    • (2003) Curr Opin Struct Biol , vol.13 , Issue.3 , pp. 317-324
    • DeRose, V.J.1
  • 18
    • 1242274330 scopus 로고    scopus 로고
    • A guide to ions and RNA structure
    • Draper DE (2004) A guide to ions and RNA structure. RNA 10(3):335-343.
    • (2004) RNA , vol.10 , Issue.3 , pp. 335-343
    • Draper, D.E.1
  • 19
    • 0027365639 scopus 로고
    • Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd
    • Duguid J, Bloomfield VA, Benevides J, Thomas GJ Jr.(1993) Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd. Biophys J 65(5):1916-1928. doi:10.1016/S0006-3495(93)81263-3.
    • (1993) Biophys J , vol.65 , Issue.5 , pp. 1916-1928
    • Duguid, J.1    Bloomfield, V.A.2    Benevides, J.3    Thomas, G.J.4
  • 20
    • 77953379568 scopus 로고    scopus 로고
    • R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript
    • Eickbush DG, Eickbush TH (2010) R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript. Mol Cell Biol 30(13):3142-3150. doi:10.1128/MCB.00300-10.
    • (2010) Mol Cell Biol , vol.30 , Issue.13 , pp. 3142-3150
    • Eickbush, D.G.1    Eickbush, T.H.2
  • 22
    • 0030798881 scopus 로고    scopus 로고
    • Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme
    • Fauzi H, Kawakami J, Nishikawa F, Nishikawa S (1997) Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme. Nucleic Acids Res 25(15):3124-3130.
    • (1997) Nucleic Acids Res , vol.25 , Issue.15 , pp. 3124-3130
    • Fauzi, H.1    Kawakami, J.2    Nishikawa, F.3    Nishikawa, S.4
  • 23
    • 67349123194 scopus 로고    scopus 로고
    • Comparative enzymology and structural biology of RNA self-cleavage
    • Fedor MJ (2009) Comparative enzymology and structural biology of RNA self-cleavage. Annu Rev Biophys 38:271-299. doi:10.1146/annurev.biophys.050708.133710.
    • (2009) Annu Rev Biophys , vol.38 , pp. 271-299
    • Fedor, M.J.1
  • 24
    • 0002198148 scopus 로고    scopus 로고
    • The role of metal ions in RNA biochemistry
    • Gestlend R, Cech T, Atkins J (eds), 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harber, NY
    • Feig AL, Uhlenbeck OC (1999) The role of metal ions in RNA biochemistry. In: Gestlend R, Cech T, Atkins J (eds) The RNA World, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harber, NY, pp 287-319.
    • (1999) The RNA World , pp. 287-319
    • Feig, A.L.1    Uhlenbeck, O.C.2
  • 25
    • 80052939924 scopus 로고    scopus 로고
    • Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules
    • Ferre-D'Amare AR (2011) Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. Philos Trans R Soc Lond B Biol Sci 366(1580):2942-2948. doi:10.1098/rstb.2011.0131.
    • (2011) Philos Trans R Soc Lond B Biol Sci , vol.366 , Issue.1580 , pp. 2942-2948
    • Ferre-d'Amare, A.R.1
  • 26
    • 0034695419 scopus 로고    scopus 로고
    • Crystallization and structure determination of a hepatitis delta virus ribozyme: Use of the RNA-binding protein U1A as a crystallization module
    • Ferre-D'Amare AR, Doudna JA (2000) Crystallization and structure determination of a hepatitis delta virus ribozyme: Use of the RNA-binding protein U1A as a crystallization module. J Mol Biol 295(3):541-556.
    • (2000) J Mol Biol , vol.295 , Issue.3 , pp. 541-556
    • Ferre-d'Amare, A.R.1    Doudna, J.A.2
  • 27
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare AR, Zhou KH, Doudna JA (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395(6702):567-574.
    • (1998) Nature , vol.395 , Issue.6702 , pp. 567-574
    • Ferre-d'Amare, A.R.1    Zhou, K.H.2    Doudna, J.A.3
  • 28
    • 70349279881 scopus 로고    scopus 로고
    • Identification of catalytic metal ion ligands in ribozymes
    • Frederiksen JK, Piccirilli JA (2009) Identification of catalytic metal ion ligands in ribozymes. Methods 49(2):148-166. doi:10.1016/j.ymeth.2009.07.005.
    • (2009) Methods , vol.49 , Issue.2 , pp. 148-166
    • Frederiksen, J.K.1    Piccirilli, J.A.2
  • 29
    • 81755171288 scopus 로고    scopus 로고
    • Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism
    • Ganguly A, Bevilacqua PC, Hammes-Schiffer S (2011) Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism. J Phys Chem Lett 2(22):2906-2911. doi:10.1021/jz2013215.
    • (2011) J Phys Chem Lett , vol.2 , Issue.22 , pp. 2906-2911
    • Ganguly, A.1    Bevilacqua, P.C.2    Hammes-schiffer, S.3
  • 30
    • 80155186850 scopus 로고    scopus 로고
    • Two distince catalytic strategies in the HDV ribozyme cleavage reaction
    • Golden BL (2011) Two distince catalytic strategies in the HDV ribozyme cleavage reaction. Biochemistry 50(44):9424-9433.
    • (2011) Biochemistry , vol.50 , Issue.44 , pp. 9424-9433
    • Golden, B.L.1
  • 31
    • 11444263264 scopus 로고    scopus 로고
    • Crystal structure of a phage twort group I ribozyme-product complex
    • Golden BL, Kim H, Chase E (2005) Crystal structure of a phage twort group I ribozyme-product complex. Nat Struct Mol Biol 12(1):82-89.
    • (2005) Nat Struct Mol Biol , vol.12 , Issue.1 , pp. 82-89
    • Golden, B.L.1    Kim, H.2    Chase, E.3
  • 32
    • 74249091547 scopus 로고    scopus 로고
    • Competition between Co(NH(3) (6)3+ and inner sphere Mg2+ ions in the HDV ribozyme
    • Gong B, Chen JH, Bevilacqua PC, Golden BL, Carey PR (2009a) Competition between Co(NH(3) (6)3+ and inner sphere Mg2+ ions in the HDV ribozyme. Biochemistry 48(50):11961-11970. doi:10.1021/bi901091v.
    • (2009) Biochemistry , vol.48 , Issue.50 , pp. 11961-11970
    • Gong, B.1    Chen, J.H.2    Bevilacqua, P.C.3    Golden, B.L.4    Carey, P.R.5
  • 33
    • 35848964370 scopus 로고    scopus 로고
    • Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography
    • Gong B, Chen JH, Chase E, Chadalavada DM, Yajima R, Golden BL, Bevilacqua PC, Carey PR (2007) Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography. J Am Chem Soc 129(43):13335-13342. doi:10.1021/ja0743893.
    • (2007) J Am Chem Soc , vol.129 , Issue.43 , pp. 13335-13342
    • Gong, B.1    Chen, J.H.2    Chase, E.3    Chadalavada, D.M.4    Yajima, R.5    Golden, B.L.6    Bevilacqua, P.C.7    Carey, P.R.8
  • 35
    • 48249121539 scopus 로고    scopus 로고
    • Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography
    • Gong B, Chen Y, Christian EL, Chen JH, Chase E, Chadalavada DM, Yajima R, Golden BL, Bevilacqua PC, Carey PR (2008) Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography. J Am Chem Soc 130(30):9670-9672. doi:10.1021/ja801861s.
    • (2008) J Am Chem Soc , vol.130 , Issue.30 , pp. 9670-9672
    • Gong, B.1    Chen, Y.2    Christian, E.L.3    Chen, J.H.4    Chase, E.5    Chadalavada, D.M.6    Yajima, R.7    Golden, B.L.8    Bevilacqua, P.C.9    Carey, P.R.10
  • 36
    • 80052557910 scopus 로고    scopus 로고
    • The glmS Ribozyme Tunes the Catalytically Critical pK(a) of Its Coenzyme Glucosamine-6-phosphate
    • Gong B, Klein DJ, Ferre-D'Amare AR, Carey PR (2011) The glmS Ribozyme Tunes the Catalytically Critical pK(a) of Its Coenzyme Glucosamine-6-phosphate. J Am Chem Soc 133(36):14188-14191. doi:10.1021/ja205185g.
    • (2011) J Am Chem Soc , vol.133 , Issue.36 , pp. 14188-14191
    • Gong, B.1    Klein, D.J.2    Ferre-d'Amare, A.R.3    Carey, P.R.4
  • 37
    • 0021013526 scopus 로고
    • The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
    • Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35(3 Pt 2):849-857.
    • (1983) Cell , vol.35 , Issue.3 , pp. 849-857
    • Guerrier-takada, C.1    Gardiner, K.2    Marsh, T.3    Pace, N.4    Altman, S.5
  • 38
    • 8644229237 scopus 로고    scopus 로고
    • Structure of the tetrahymena ribozyme: Base triple sandwhich and metal ion at the active site
    • Guo F, Gooding A, Cech TR (2004) Structure of the tetrahymena ribozyme: Base triple sandwhich and metal ion at the active site. Mol Cell 16(3):351-362.
    • (2004) Mol Cell , vol.16 , Issue.3 , pp. 351-362
    • Guo, F.1    Gooding, A.2    Cech, T.R.3
  • 39
    • 70349095576 scopus 로고    scopus 로고
    • Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation
    • Guo M, Spitale RC, Volpini R, Krucinska J, Cristalli G, Carey PR, Wedekind JE (2009) Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. J Am Chem Soc 131(36):12908-12909. doi:10.1021/ja9060883.
    • (2009) J Am Chem Soc , vol.131 , Issue.36 , pp. 12908-12909
    • Guo, M.1    Spitale, R.C.2    Volpini, R.3    Krucinska, J.4    Cristalli, G.5    Carey, P.R.6    Wedekind, J.E.7
  • 40
    • 3342915806 scopus 로고    scopus 로고
    • Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme
    • Harris DA, Tinsley RA, Walter NG (2004) Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme. J Mol Biol 341(2):389-403. doi:10.1016/j.jmb.2004.05.074.
    • (2004) J Mol Biol , vol.341 , Issue.2 , pp. 389-403
    • Harris, D.A.1    Tinsley, R.A.2    Walter, N.G.3
  • 41
    • 0034612331 scopus 로고    scopus 로고
    • Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
    • Isambert H, Siggia ED (2000) Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc Natl Acad Sci USA 97(12):6515-6520. doi:10.1073/ pnas.110533697.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.12 , pp. 6515-6520
    • Isambert, H.1    Siggia, E.D.2
  • 43
    • 2442641641 scopus 로고    scopus 로고
    • A conformational switch controls hepatitis delta virus ribozyme catalysis
    • Ke A, Zhou K, Ding F, Cate JH, Doudna JA (2004) A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429(6988):201-205.
    • (2004) Nature , vol.429 , Issue.6988 , pp. 201-205
    • Ke, A.1    Zhou, K.2    Ding, F.3    Cate, J.H.4    Doudna, J.A.5
  • 44
    • 36849061230 scopus 로고    scopus 로고
    • Essential role of an active-site guanine in glmS ribozyme catalysis
    • Klein DJ, Been MD, Ferre-D'Amare AR (2007) Essential role of an active-site guanine in glmS ribozyme catalysis. J Am Chem Soc 129(48):14858-14859. doi:10.1021/ja0768441.
    • (2007) J Am Chem Soc , vol.129 , Issue.48 , pp. 14858-14859
    • Klein, D.J.1    Been, M.D.2    Ferre-d'Amare, A.R.3
  • 45
    • 33748325570 scopus 로고    scopus 로고
    • Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
    • Klein DJ, Ferre-D'Amare AR (2006) Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313(5794):1752-1756. doi:10.1126/science.1129666.
    • (2006) Science , vol.313 , Issue.5794 , pp. 1752-1756
    • Klein, D.J.1    Ferre-d'Amare, A.R.2
  • 46
    • 23444456517 scopus 로고    scopus 로고
    • Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
    • Krasovska MV, Sefcikova J, Spackova N, Sponer J, Walter NG (2005) Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J Mol Biol 351(4):731-748. doi:10.1016/j.jmb.2005.06.016.
    • (2005) J Mol Biol , vol.351 , Issue.4 , pp. 731-748
    • Krasovska, M.V.1    Sefcikova, J.2    Spackova, N.3    Sponer, J.4    Walter, N.G.5
  • 47
    • 0020417286 scopus 로고
    • Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena
    • Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31(1):147-157.
    • (1982) Cell , vol.31 , Issue.1 , pp. 147-157
    • Kruger, K.1    Grabowski, P.J.2    Zaug, A.J.3    Sands, J.4    Gottschling, D.E.5    Cech, T.R.6
  • 48
    • 0024209351 scopus 로고
    • Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus
    • Kuo MY, Sharmeen L, Dinter-Gottlieb G, Taylor J (1988) Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J Virol 62(12):4439-4444.
    • (1988) J Virol , vol.62 , Issue.12 , pp. 4439-4444
    • Kuo, M.Y.1    Sharmeen, L.2    Dinter-gottlieb, G.3    Taylor, J.4
  • 49
    • 0004288043 scopus 로고    scopus 로고
    • John Wiley & Sons, Ltd
    • Long DA (2002) The Raman effect. John Wiley & Sons, Ltd. doi:10.1002/0470845767.
    • (2002) The Raman effect
    • Long, D.A.1
  • 50
    • 0035812381 scopus 로고    scopus 로고
    • Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme
    • Luptak A, Ferre-D'Amare AR, Zhou K, Zilm KW, Doudna JA (2001) Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme. J Am Chem Soc 123(35):8447-8452.
    • (2001) J Am Chem Soc , vol.123 , Issue.35 , pp. 8447-8452
    • Luptak, A.1    Ferre-d'Amare, A.R.2    Zhou, K.3    Zilm, K.W.4    Doudna, J.A.5
  • 51
    • 0017882656 scopus 로고
    • Heavy metal-nucleotide interactions. 12. Competitive reactions in systems of far nudeotides with cis- and trans-diamine platinum (II). Raman difference spectrophatometric determination of the relative nucleophilicity of guanine, cytidine, adenosine and uridine monophosphates as well as the analogous bases in DNA
    • Mansy S, Chu G.Y-H, Ducan RE, Tobias RS (1978). Heavy metal-nucleotide interactions. 12. Competitive reactions in systems of far nudeotides with cis- and trans-diamine platinum (II). Raman difference spectrophatometric determination of the relative nucleophilicity of guanine, cytidine, adenosine and uridine monophosphates as well as the analogous bases in DNA. J Am Chen Soc 100(2): 607-616.
    • (1978) J Am Chen Soc , vol.100 , Issue.2 , pp. 607-616
    • Mansy, S.1    Chu, G.Y.-H.2    Ducan, R.E.3    Tobias, R.S.4
  • 52
    • 33746228126 scopus 로고    scopus 로고
    • Tertiary contacts distant from the active site prime a ribozyme for catalysis
    • Martick M, Scott WG (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126(2):309-320. doi:10.1016/j.cell.2006.06.036.
    • (2006) Cell , vol.126 , Issue.2 , pp. 309-320
    • Martick, M.1    Scott, W.G.2
  • 53
    • 0019210870 scopus 로고
    • Heavy metal-nucleotide interactions. 14. Raman difference spectrophometric studies of competitive reactions in mixtures of four nucleotides with electrophiles. Factors governing selectivity in the binding reaction
    • Moller MR, Bruck MA, O'Connor T, Armatis FJ, Edward A Jr.(1980) Heavy metal-nucleotide interactions. 14. Raman difference spectrophometric studies of competitive reactions in mixtures of four nucleotides with electrophiles. Factors governing selectivity in the binding reaction. J Am Chem Soc 102(14):4589-4598.
    • (1980) J Am Chem Soc , vol.102 , Issue.14 , pp. 4589-4598
    • Moller, M.R.1    Bruck, M.A.2    O'Connor, T.3    Armatis, F.J.4    Edward, A.5
  • 54
    • 33947356675 scopus 로고    scopus 로고
    • Mechanistic characterization of the HDV genomic ribozyme: A mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons
    • Nakano S, Bevilacqua PC (2007) Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons. Biochemistry 46(11):3001-3012. doi:10.1021/bi061732s.
    • (2007) Biochemistry , vol.46 , Issue.11 , pp. 3001-3012
    • Nakano, S.1    Bevilacqua, P.C.2
  • 55
    • 0037452909 scopus 로고    scopus 로고
    • Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism
    • Nakano S, Cerrone AL, Bevilacqua PC (2003) Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry 42(10):2982-2994. doi:10.1021/bi026815x.
    • (2003) Biochemistry , vol.42 , Issue.10 , pp. 2982-2994
    • Nakano, S.1    Cerrone, A.L.2    Bevilacqua, P.C.3
  • 56
    • 0034712097 scopus 로고    scopus 로고
    • General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
    • Nakano S, Chadalavada DM, Bevilacqua PC (2000) General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 287(5457):1493-1497.
    • (2000) Science , vol.287 , Issue.5457 , pp. 1493-1497
    • Nakano, S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 57
    • 0035833978 scopus 로고    scopus 로고
    • Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism
    • Nakano S, Proctor DJ, Bevilacqua PC (2001) Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry 40(40):12022-12038.
    • (2001) Biochemistry , vol.40 , Issue.40 , pp. 12022-12038
    • Nakano, S.1    Proctor, D.J.2    Bevilacqua, P.C.3
  • 58
    • 0035001461 scopus 로고    scopus 로고
    • Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations
    • O'Rear JL, Wang S, Feig AL, Beigelman L, Uhlenbeck OC, Herschlag D (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA 7(4):537-545.
    • (2001) RNA , vol.7 , Issue.4 , pp. 537-545
    • O'Rear, J.L.1    Wang, S.2    Feig, A.L.3    Beigelman, L.4    Uhlenbeck, O.C.5    Herschlag, D.6
  • 59
    • 0037133526 scopus 로고    scopus 로고
    • pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping
    • Oyelere AK, Kardon JR, Strobel SA (2002) pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping. Biochemistry 41(11):3667-3675.
    • (2002) Biochemistry , vol.41 , Issue.11 , pp. 3667-3675
    • Oyelere, A.K.1    Kardon, J.R.2    Strobel, S.A.3
  • 60
    • 1842525548 scopus 로고
    • A Raman spectroscopic investigation of the magesnium nitrate-water system
    • Peleg M (1972) A Raman spectroscopic investigation of the magesnium nitrate-water system. J Phys Chem 76:1019-1025.
    • (1972) J Phys Chem , vol.76 , pp. 1019-1025
    • Peleg, M.1
  • 61
    • 0037154091 scopus 로고    scopus 로고
    • Reaction pathway of the trans-acting hepatitis delta virus ribozyme: A conformational change accompanies catalysis
    • Pereira MJ, Harris DA, Rueda D, Walter NG (2002) Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis. Biochemistry 41(3):730-740.
    • (2002) Biochemistry , vol.41 , Issue.3 , pp. 730-740
    • Pereira, M.J.1    Harris, D.A.2    Rueda, D.3    Walter, N.G.4
  • 62
    • 0025882069 scopus 로고
    • A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA
    • Perrotta AT, Been MD (1991) A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature 350(6317):434-436. doi:10.1038/350434a0.
    • (1991) Nature , vol.350 , Issue.6317 , pp. 434-436
    • Perrotta, A.T.1    Been, M.D.2
  • 63
    • 0033215448 scopus 로고    scopus 로고
    • Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
    • Perrotta AT, Shih I, Been MD (1999) Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science 286(5437):123-126.
    • (1999) Science , vol.286 , Issue.5437 , pp. 123-126
    • Perrotta, A.T.1    Shih, I.2    Been, M.D.3
  • 64
    • 33745627769 scopus 로고    scopus 로고
    • Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme
    • Perrotta AT, Wadkins TS, Been MD (2006) Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme. RNA 12(7):1282-1291. doi:10.1261/ rna.14106.
    • (2006) RNA , vol.12 , Issue.7 , pp. 1282-1291
    • Perrotta, A.T.1    Wadkins, T.S.2    Been, M.D.3
  • 65
    • 0000574250 scopus 로고    scopus 로고
    • An ab initio and Raman investigation of magnesium(II) hydration
    • Pye CC, Rudolph WW (1998) An ab initio and Raman investigation of magnesium(II) hydration. J Phys Chem A 102(48):9933-9943.
    • (1998) J Phys Chem A , vol.102 , Issue.48 , pp. 9933-9943
    • Pye, C.C.1    Rudolph, W.W.2
  • 66
    • 0034602648 scopus 로고    scopus 로고
    • A host-specific function is required for ligation of a wide variety of ribozyme-processed RNAs
    • Reid CE, Lazinski DW (2000) A host-specific function is required for ligation of a wide variety of ribozyme-processed RNAs. Proc Natl Acad Sci USA 97(1):424-429.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.1 , pp. 424-429
    • Reid, C.E.1    Lazinski, D.W.2
  • 67
    • 78650175123 scopus 로고    scopus 로고
    • Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA
    • Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragon A (2010) Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 468(7325):784-789. doi:10.1038/nature09516.
    • (2010) Nature , vol.468 , Issue.7325 , pp. 784-789
    • Reiter, N.J.1    Osterman, A.2    Torres-larios, A.3    Swinger, K.K.4    Pan, T.5    Mondragon, A.6
  • 68
    • 0025082875 scopus 로고
    • Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions
    • Rosenstein SP, Been MD (1990) Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions. Biochemistry 29(35):8011-8016.
    • (1990) Biochemistry , vol.29 , Issue.35 , pp. 8011-8016
    • Rosenstein, S.P.1    Been, M.D.2
  • 69
    • 0035848837 scopus 로고    scopus 로고
    • Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
    • Rupert PB, Ferre-D'Amare AR (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410(6830):780-786.
    • (2001) Nature , vol.410 , Issue.6830 , pp. 780-786
    • Rupert, P.B.1    Ferre-d'Amare, A.R.2
  • 70
    • 33749034196 scopus 로고    scopus 로고
    • A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene
    • Salehi-Ashtiani K, Luptak A, Litovchick A, Szostak JW (2006) A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 313(5794):1788-1792. doi:10.1126/science.1129308.
    • (2006) Science , vol.313 , Issue.5794 , pp. 1788-1792
    • Salehi-ashtiani, K.1    Luptak, A.2    Litovchick, A.3    Szostak, J.W.4
  • 71
    • 0035498871 scopus 로고    scopus 로고
    • In vitro evolution suggests multiple origins for the hammerhead ribozyme
    • Salehi-Ashtiani K, Szostak JW (2001) In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature 414(6859):82-84. doi:10.1038/35102081.
    • (2001) Nature , vol.414 , Issue.6859 , pp. 82-84
    • Salehi-ashtiani, K.1    Szostak, J.W.2
  • 72
    • 77955776847 scopus 로고    scopus 로고
    • RNase footprinting demonstrates antigenomic hepatitis delta virus ribozyme structural rearrangement as a result of self-cleavage reaction
    • Savochkina L, Alekseenkova V, Belyanko T, Dobrynina N, Beabealashvilli R (2008) RNase footprinting demonstrates antigenomic hepatitis delta virus ribozyme structural rearrangement as a result of self-cleavage reaction. BMC Res Notes 1:15. doi:10.1186/1756-0500-1-15.
    • (2008) BMC Res Notes , vol.1 , pp. 15
    • Savochkina, L.1    Alekseenkova, V.2    Belyanko, T.3    Dobrynina, N.4    Beabealashvilli, R.5
  • 73
    • 0023747377 scopus 로고
    • Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage
    • Sharmeen L, Kuo MY, Dinter-Gottlieb G, Taylor J (1988) Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 62(8):2674-2679.
    • (1988) J Virol , vol.62 , Issue.8 , pp. 2674-2679
    • Sharmeen, L.1    Kuo, M.Y.2    Dinter-gottlieb, G.3    Taylor, J.4
  • 74
    • 0035801474 scopus 로고    scopus 로고
    • Energetic contribution of non-essential 5S sequence to catalysis in a hepatitis delta virus ribozyme
    • Shih IH, Been MD (2001a) Energetic contribution of non-essential 5S sequence to catalysis in a hepatitis delta virus ribozyme. EMBO J 20(17):4884-4891. doi:10.1093/emboj/20.17.4884.
    • (2001) EMBO J , vol.20 , Issue.17 , pp. 4884-4891
    • Shih, I.H.1    Been, M.D.2
  • 75
    • 0035852640 scopus 로고    scopus 로고
    • Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage
    • Shih IH, Been MD (2001b) Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. Proc Natl Acad Sci USA 98(4):1489-1494. doi:10.1073/pnas.98.4.1489.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.4 , pp. 1489-1494
    • Shih, I.H.1    Been, M.D.2
  • 76
    • 0026035592 scopus 로고
    • Antigenomic Hepatitis delta virus ribozymes self-cleave in 18 M formamide
    • Smith JB, Dinter-Gottlieb G (1991) Antigenomic Hepatitis delta virus ribozymes self-cleave in 18 M formamide. Nucleic Acids Res 19(6):1285-1289.
    • (1991) Nucleic Acids Res , vol.19 , Issue.6 , pp. 1285-1289
    • Smith, J.B.1    Dinter-gottlieb, G.2
  • 77
    • 0027184481 scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90(14):6498-6502.
    • (1993) Proc Natl Acad Sci USA , vol.90 , Issue.14 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 78
    • 0032516471 scopus 로고    scopus 로고
    • Unusual metal ion catalysis in an acyl-transferase ribozyme
    • Suga H, Cowan JA, Szostak JW (1998) Unusual metal ion catalysis in an acyl-transferase ribozyme. Biochemistry 37(28):10118-10125. doi:10.1021/bi980432a.
    • (1998) Biochemistry , vol.37 , Issue.28 , pp. 10118-10125
    • Suga, H.1    Cowan, J.A.2    Szostak, J.W.3
  • 79
    • 0001854341 scopus 로고
    • Laser Raman spectroscopy of nucleic acids
    • Thomas GJ, Tsuboi M (1993) Laser Raman spectroscopy of nucleic acids. Adv Biophys Chem 3:1-70.
    • (1993) Adv Biophys Chem , vol.3 , pp. 1-70
    • Thomas, G.J.1    Tsuboi, M.2
  • 80
    • 3142746008 scopus 로고    scopus 로고
    • Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme
    • Tinsley RA, Harris DA, Walter NG (2004) Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme. Biochemistry 43(28):8935-8945. doi:10.1021/bi049471e.
    • (2004) Biochemistry , vol.43 , Issue.28 , pp. 8935-8945
    • Tinsley, R.A.1    Harris, D.A.2    Walter, N.G.3
  • 81
    • 41749109563 scopus 로고    scopus 로고
    • Crystal structure of a self-spliced group II intron
    • Toor N, Keating KS, Taylor SD, Pyle AM (2008) Crystal structure of a self-spliced group II intron. Science 320(5872):77-82. doi:10.1126/science.1153803.
    • (2008) Science , vol.320 , Issue.5872 , pp. 77-82
    • Toor, N.1    Keating, K.S.2    Taylor, S.D.3    Pyle, A.M.4
  • 82
    • 77956170803 scopus 로고    scopus 로고
    • Long-distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments
    • Veeraraghavan N, Bevilacqua PC, Hammes-Schiffer S (2010) Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments. J Mol Biol 402(1):278-291. doi:10.1016/j.jmb.2010.07.025.
    • (2010) J Mol Biol , vol.402 , Issue.1 , pp. 278-291
    • Veeraraghavan, N.1    Bevilacqua, P.C.2    Hammes-schiffer, S.3
  • 83
    • 79953205188 scopus 로고    scopus 로고
    • Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions
    • Veeraraghavan N, Ganguly A, Chen JH, Bevilacqua PC, Hammes-Schiffer S, Golden BL (2011a) Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry 50(13):2672-2682. doi:10.1021/bi2000164.
    • (2011) Biochemistry , vol.50 , Issue.13 , pp. 2672-2682
    • Veeraraghavan, N.1    Ganguly, A.2    Chen, J.H.3    Bevilacqua, P.C.4    Hammes-schiffer, S.5    Golden, B.L.6
  • 84
    • 79959537078 scopus 로고    scopus 로고
    • Mechanistic Strategies in the HDV Ribozyme: Chelated and Diffuse Metal Ion Interactions and Active Site Protonation
    • Veeraraghavan N, Ganguly A, Golden BL, Bevilacqua PC, Hammes-Schiffer S (2011b) Mechanistic Strategies in the HDV Ribozyme: Chelated and Diffuse Metal Ion Interactions and Active Site Protonation. J Phys Chem B. doi:10.1021/jp203202e.
    • (2011) J Phys Chem B
    • Veeraraghavan, N.1    Ganguly, A.2    Golden, B.L.3    Bevilacqua, P.C.4    Hammes-schiffer, S.5
  • 86
    • 0036161836 scopus 로고    scopus 로고
    • Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus
    • Wadkins TS, Been MD (2002) Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus. Cellular and molecular life sciences: CMLS 59(1):112-125.
    • (2002) Cellular and molecular life sciences: CMLS , vol.59 , Issue.1 , pp. 112-125
    • Wadkins, T.S.1    Been, M.D.2
  • 87
    • 0033053643 scopus 로고    scopus 로고
    • A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes
    • Wadkins TS, Perrotta AT, Ferre-D'Amare AR, Doudna JA, Been MD (1999) A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA 5(6):720-727.
    • (1999) RNA , vol.5 , Issue.6 , pp. 720-727
    • Wadkins, T.S.1    Perrotta, A.T.2    Ferre-d'Amare, A.R.3    Doudna, J.A.4    Been, M.D.5
  • 88
    • 0035793217 scopus 로고    scopus 로고
    • A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion
    • Wadkins TS, Shih I, Perrotta AT, Been MD (2001) A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion. J Mol Biol 305(5):1045-1055. doi:10.1006/jmbi.2000.4368.
    • (2001) J Mol Biol , vol.305 , Issue.5 , pp. 1045-1055
    • Wadkins, T.S.1    Shih, I.2    Perrotta, A.T.3    Been, M.D.4
  • 89
    • 80052822183 scopus 로고    scopus 로고
    • HDV-like self-cleaving ribozymes
    • Webb CH, Luptak A (2011) HDV-like self-cleaving ribozymes. RNA Biol 8(5).
    • (2011) RNA Biol , vol.8 , Issue.5
    • Webb, C.H.1    Luptak, A.2
  • 90
    • 72449145407 scopus 로고    scopus 로고
    • Widespread occurrence of self-cleaving ribozymes
    • Webb CH, Riccitelli NJ, Ruminski DJ, Luptak A (2009) Widespread occurrence of self-cleaving ribozymes Science 326(5955):953. doi:10.1126/science.1178084.
    • (2009) Science , vol.326 , Issue.5955 , pp. 953
    • Webb, C.H.1    Riccitelli, N.J.2    Ruminski, D.J.3    Luptak, A.4
  • 91
    • 0032853242 scopus 로고    scopus 로고
    • In vitro selection of functional nucleic acids
    • Wilson DS, Szostak JW (1999) In vitro selection of functional nucleic acids. Annu Rev Biochem 68:611-647. doi:10.1146/annurev.biochem.68.1.611.
    • (1999) Annu Rev Biochem , vol.68 , pp. 611-647
    • Wilson, D.S.1    Szostak, J.W.2
  • 92


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.