메뉴 건너뛰기




Volumn 14, Issue 10, 2008, Pages 2125-2135

Effects of N2,N2-dimethylguanosine on RNA structure and stability: Crystal structure of an RNA duplex with tandem m2 2G:A pairs

Author keywords

Base mismatch; Hydration; RNA methylation; RNA stability; X ray crystallography

Indexed keywords

ALANINE; DIMETHYLGUANOSINE; GLYCINE; GUANINE; GUANOSINE; MESSENGER RNA; TRANSFER RNA; UNCLASSIFIED DRUG; ADENINE; DRUG DERIVATIVE; N(2),N(2) DIMETHYLGUANOSINE; N(2),N(2)-DIMETHYLGUANOSINE; RNA;

EID: 52949125637     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1078508     Document Type: Article
Times cited : (35)

References (47)
  • 1
    • 0029822046 scopus 로고    scopus 로고
    • Baeyens, K.J., De Bondt, H.L., Pardi, A., and Holbrook, S.R. 1996. A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing. Proc. Natl. Acad. Sci. 93: 12851-12855.
    • Baeyens, K.J., De Bondt, H.L., Pardi, A., and Holbrook, S.R. 1996. A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing. Proc. Natl. Acad. Sci. 93: 12851-12855.
  • 2
    • 0030132944 scopus 로고    scopus 로고
    • A highly efficient 24-condition matrix for the crystallization of nucleic acid fragments
    • Berger, I., Kang, C.H., Sinha, N., Wolters, M., and Rich, A. 1996. A highly efficient 24-condition matrix for the crystallization of nucleic acid fragments. Acta Crystallogr. D Biol. Crystallogr. 52: 465-468.
    • (1996) Acta Crystallogr. D Biol. Crystallogr , vol.52 , pp. 465-468
    • Berger, I.1    Kang, C.H.2    Sinha, N.3    Wolters, M.4    Rich, A.5
  • 3
    • 28844509141 scopus 로고    scopus 로고
    • Mechanism of hairpin-duplex conversion for the HIV-1 dimerization initiation site
    • Bernacchi, S., Ennifar, E., Tóth, K., Walter, P., Langowski, J., and Dumas, P. 2005. Mechanism of hairpin-duplex conversion for the HIV-1 dimerization initiation site. J. Biol. Chem. 280: 40112-40121.
    • (2005) J. Biol. Chem , vol.280 , pp. 40112-40121
    • Bernacchi, S.1    Ennifar, E.2    Tóth, K.3    Walter, P.4    Langowski, J.5    Dumas, P.6
  • 4
    • 37549003235 scopus 로고    scopus 로고
    • Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: Thermodynamics and effect on the kissing-loop to duplex conversion
    • Bernacchi, S., Freisz, S., Maechling, C., Spiess, B., Marquet, R., Dumas, P., and Ennifar, E. 2007. Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: Thermodynamics and effect on the kissing-loop to duplex conversion. Nucleic Acids Res. 35: 7128-7139.
    • (2007) Nucleic Acids Res , vol.35 , pp. 7128-7139
    • Bernacchi, S.1    Freisz, S.2    Maechling, C.3    Spiess, B.4    Marquet, R.5    Dumas, P.6    Ennifar, E.7
  • 7
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • 4
    • CCP4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
    • (1994) Acta Crystallogr. D Biol. Crystallogr , vol.50 , pp. 760-763
    • CCP1
  • 8
    • 14344256105 scopus 로고    scopus 로고
    • Solution structure of an RNA internal loop with three consecutive sheared GA pairs
    • Chen, G., Znosko, B.M., Kennedy, S.D., Schroeder, S.J., Krugh, T.R., and Turner, D.H. 2005. Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry 45: 2845-2856.
    • (2005) Biochemistry , vol.45 , pp. 2845-2856
    • Chen, G.1    Znosko, B.M.2    Kennedy, S.D.3    Schroeder, S.J.4    Krugh, T.R.5    Turner, D.H.6
  • 9
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
    • Correll, C.C., Freeborn, B., Moore, P.B., and Steitz, T.A. 1997. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91: 705-712.
    • (1997) Cell , vol.91 , pp. 705-712
    • Correll, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 11
    • 0028988341 scopus 로고
    • Enzymatic formation of N2,N2-dimethylguanosine in eukaryotic tRNA: Importance of the tRNA architecture
    • Edqvist, J., Sträby, K.B., and Grosjean, H. 1995. Enzymatic formation of N2,N2-dimethylguanosine in eukaryotic tRNA: Importance of the tRNA architecture. Biochimie 77: 53-60.
    • (1995) Biochimie , vol.77 , pp. 53-60
    • Edqvist, J.1    Sträby, K.B.2    Grosjean, H.3
  • 12
    • 0029956116 scopus 로고    scopus 로고
    • RNA hydration: A detailed look
    • Egli, M., Portmann, S., and Usman, N. 1996. RNA hydration: A detailed look. Biochemistry 35: 8489-8494.
    • (1996) Biochemistry , vol.35 , pp. 8489-8494
    • Egli, M.1    Portmann, S.2    Usman, N.3
  • 13
    • 34548367542 scopus 로고    scopus 로고
    • Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding
    • Ennifar, E., Bernacchi, S., Wolff, P., and Dumas, P. 2007. Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding. RNA 13: 1445-1452.
    • (2007) RNA , vol.13 , pp. 1445-1452
    • Ennifar, E.1    Bernacchi, S.2    Wolff, P.3    Dumas, P.4
  • 14
    • 0003634460 scopus 로고    scopus 로고
    • Grosjean, H. and Benne, R, eds, ASM Press, Washington, DC
    • Grosjean, H. and Benne, R., eds. 1998. Modification and editing of RNA. ASM Press, Washington, DC.
    • (1998) Modification and editing of RNA
  • 15
    • 0031559569 scopus 로고    scopus 로고
    • The detailed structure of tandem G.A mismatched base-pair motifs in RNA duplexes is context dependent
    • Heus, H.A., Wijmenga, S.S., Hoppe, H., and Hilbers, C.W. 1997. The detailed structure of tandem G.A mismatched base-pair motifs in RNA duplexes is context dependent. J. Mol. Biol. 271: 147-158.
    • (1997) J. Mol. Biol , vol.271 , pp. 147-158
    • Heus, H.A.1    Wijmenga, S.S.2    Hoppe, H.3    Hilbers, C.W.4
  • 16
    • 0037084222 scopus 로고    scopus 로고
    • RNA two-state conformation equilibria and the effect of nucleobase methylation
    • Höbartner, C., Ebert, M.-O., Jaun, B., and Micura, R. 2002. RNA two-state conformation equilibria and the effect of nucleobase methylation. Angew. Chem. Int. Ed. 41: 605-609.
    • (2002) Angew. Chem. Int. Ed , vol.41 , pp. 605-609
    • Höbartner, C.1    Ebert, M.-O.2    Jaun, B.3    Micura, R.4
  • 20
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • Lavery, R. and Sklenar, H. 1989. Defining the structure of irregular nucleic acids: Conventions and principles. J. Biomol. Struct. Dyn. 6: 655-667.
    • (1989) J. Biomol. Struct. Dyn , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 21
    • 0028773639 scopus 로고
    • Crystal and molecular structure of r(CGCGAAUUAGCG): An RNA duplex containing two G(anti).A(anti) base pairs
    • Leonard, G.A., McAuley-Hecht, K.E., Ebel, S., Lough, D.M., Brown, T., and Hunter, W.N. 1994. Crystal and molecular structure of r(CGCGAAUUAGCG): An RNA duplex containing two G(anti).A(anti) base pairs. Structure 2: 483-494.
    • (1994) Structure , vol.2 , pp. 483-494
    • Leonard, G.A.1    McAuley-Hecht, K.E.2    Ebel, S.3    Lough, D.M.4    Brown, T.5    Hunter, W.N.6
  • 23
    • 36148961231 scopus 로고    scopus 로고
    • Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribodifluorotoluyl nucleotide: Insights into substrate requirements by the human RISC Ago2 enzyme
    • Li, F., Pallan, P.S., Maier, M.A., Rajeev, K.G., Mathieu, S.L., Kreutz, C., Fan, Y., Sanghvi, J., Micura, R., Rozners, E., et al. 2007. Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribodifluorotoluyl nucleotide: Insights into substrate requirements by the human RISC Ago2 enzyme. Nucleic Acids Res. 35: 6424-6438.
    • (2007) Nucleic Acids Res , vol.35 , pp. 6424-6438
    • Li, F.1    Pallan, P.S.2    Maier, M.A.3    Rajeev, K.G.4    Mathieu, S.L.5    Kreutz, C.6    Fan, Y.7    Sanghvi, J.8    Micura, R.9    Rozners, E.10
  • 24
    • 0035476599 scopus 로고    scopus 로고
    • Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion
    • Micura, R., Pils, W., Höbartner, C., Grubmayr, K., Ebert, M.-O., and Jaun, B. 2001. Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion. Nucleic Acids Res. 29: 3997-4005.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3997-4005
    • Micura, R.1    Pils, W.2    Höbartner, C.3    Grubmayr, K.4    Ebert, M.-O.5    Jaun, B.6
  • 25
    • 33646806139 scopus 로고    scopus 로고
    • 5C methyltransferase specific for 16 S rRNA nucleotide 1407
    • 5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359: 777-786.
    • (2006) J. Mol. Biol , vol.359 , pp. 777-786
    • Møller Andersen, N.1    Douthwaite, S.2
  • 26
    • 0028897382 scopus 로고
    • Purine-purine mismatches in RNA helices: Evidence for protonated G.A pairs and next-nearest neighbor effects
    • Morse, S.E. and Draper, D.E. 1995. Purine-purine mismatches in RNA helices: Evidence for protonated G.A pairs and next-nearest neighbor effects. Nucleic Acids Res. 23: 302-306.
    • (1995) Nucleic Acids Res , vol.23 , pp. 302-306
    • Morse, S.E.1    Draper, D.E.2
  • 30
    • 0035692119 scopus 로고    scopus 로고
    • Reliable chemical synthesis of oligoribonucleotides (RNA) with 2′-O- [(triisopropylsilyl)oxy]methyl (2′-O-tom) protected phosphoramidites
    • Pitsch, S., Weiss, P.A., Jenny, L., Stutz, A., and Wu, X. 2001. Reliable chemical synthesis of oligoribonucleotides (RNA) with 2′-O- [(triisopropylsilyl)oxy]methyl (2′-O-tom) protected phosphoramidites. Helv. Chim. Acta 84: 3773-3795.
    • (2001) Helv. Chim. Acta , vol.84 , pp. 3773-3795
    • Pitsch, S.1    Weiss, P.A.2    Jenny, L.3    Stutz, A.4    Wu, X.5
  • 32
    • 0032529298 scopus 로고    scopus 로고
    • 2-Methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops
    • 2-Methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops. Nucleic Acids Res. 26: 3640-3644.
    • (1998) Nucleic Acids Res , vol.26 , pp. 3640-3644
    • Rife, J.P.1    Cheng, C.S.2    Moore, P.B.3    Strobel, S.A.4
  • 35
    • 0027146665 scopus 로고
    • 2 in solution from NMR and restrained molecular dynamics
    • 2 in solution from NMR and restrained molecular dynamics. Biochemistry 32: 12612-12623.
    • (1993) Biochemistry , vol.32 , pp. 12612-12623
    • SantaLucia Jr., J.1    Turner, D.H.2
  • 36
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
    • Schuettelkopf, A.W. and van Aalten, D.M.F. 2004. PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60: 1355-1363.
    • (2004) Acta Crystallogr. D Biol. Crystallogr , vol.60 , pp. 1355-1363
    • Schuettelkopf, A.W.1    van Aalten, D.M.F.2
  • 38
    • 34249856379 scopus 로고    scopus 로고
    • Ribosomal RNA guanine-(N2)-methyltransferases and their targets
    • Sergiev, P.V., Bogdanov, A.A., and Dontsova, O.A. 2007. Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Nucleic Acids Res. 35: 2295-2301.
    • (2007) Nucleic Acids Res , vol.35 , pp. 2295-2301
    • Sergiev, P.V.1    Bogdanov, A.A.2    Dontsova, O.A.3
  • 39
    • 0033862354 scopus 로고    scopus 로고
    • The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited
    • Shi, H. and Moore, P.B. 2000. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited. RNA 6: 1091-1105.
    • (2000) RNA , vol.6 , pp. 1091-1105
    • Shi, H.1    Moore, P.B.2
  • 40
    • 0029400768 scopus 로고
    • 2-dimethylguanosine presence and alternate tRNA conformers
    • 2-dimethylguanosine presence and alternate tRNA conformers. RNA 1: 886-891.
    • (1995) RNA , vol.1 , pp. 886-891
    • Steinberg, S.1    Cedergren, R.2
  • 41
    • 36248946677 scopus 로고    scopus 로고
    • Conversion of stable RNA hairpin to a metastable dimer in frozen solution
    • Sun, X., Li, J.M., and Wartell, R.M. 2007. Conversion of stable RNA hairpin to a metastable dimer in frozen solution. RNA 13: 2277-2286.
    • (2007) RNA , vol.13 , pp. 2277-2286
    • Sun, X.1    Li, J.M.2    Wartell, R.M.3
  • 43
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • Vagin, A. and Teplyakov, A. 1997. MOLREP: An automated program for molecular replacement. J. Appl. Crystallogr. 30: 1022-1025.
    • (1997) J. Appl. Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 44
    • 34548518530 scopus 로고    scopus 로고
    • The 2 Å structure of helix 6 of the human signal recognition particle RNA
    • Wild, K., Weichenrieder, O., Leonard, G.A., and Cusack, S. 1999. The 2 Å structure of helix 6 of the human signal recognition particle RNA. Structure 7: 1345-1352.
    • (1999) Structure , vol.7 , pp. 1345-1352
    • Wild, K.1    Weichenrieder, O.2    Leonard, G.A.3    Cusack, S.4
  • 45
    • 0035182073 scopus 로고    scopus 로고
    • Use of TLS parameters to model anisotropic displacements in macromolecular refinement
    • Winn, M.D., Isupov, M.N., and Murshudov, G.N. 2001. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 57: 122-133.
    • (2001) Acta Crystallogr. D Biol. Crystallogr , vol.57 , pp. 122-133
    • Winn, M.D.1    Isupov, M.N.2    Murshudov, G.N.3
  • 46
    • 0029744135 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry 35: 9677-9689.
    • (1996) Biochemistry , vol.35 , pp. 9677-9689
    • Wu, M.1    Turner, D.H.2
  • 47
    • 0030929777 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry 36: 4449-4460.
    • (1997) Biochemistry , vol.36 , pp. 4449-4460
    • Wu, M.1    SantaLucia Jr., J.2    Turner, D.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.