메뉴 건너뛰기




Volumn 48, Issue 29, 2009, Pages 6988-6997

Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B

Author keywords

[No Author keywords available]

Indexed keywords

AMINOGLYCOSIDE; CONTACT POINTS; DNA SYNTHESIS; FT-ICR MASS SPECTROMETRY; HIGH RESOLUTION; ISOTHERMAL TITRATION CALORIMETRY; MOLECULAR MECHANISM; RETROTRANSPOSON; REVERSE TRANSCRIPTASES; RIBONUCLEOTIDES; RNA-DNA HYBRIDS; RNASE H; SACCHAROMYCES CEREVISIAE; SEQUENCE SIMILARITY; SPECIFIC RECOGNITION; STRUCTURAL FEATURE; SUBDOMAIN; SUBSTRATE BINDING;

EID: 67651235535     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi900357j     Document Type: Article
Times cited : (17)

References (36)
  • 1
    • 0000553844 scopus 로고
    • Roles of ribonuclease H in reverse transcription
    • Skalka, A. M, and Goff, S. P, Eds, pp, Cold Spring Harbor Laboratory Press, Plainview, NY
    • Champoux, J. J. (1993) Roles of ribonuclease H in reverse transcription. In Reverse Transcriptase (Skalka, A. M., and Goff, S. P., Eds.) pp 103-118, Cold Spring Harbor Laboratory Press, Plainview, NY.
    • (1993) Reverse Transcriptase , pp. 103-118
    • Champoux, J.J.1
  • 3
    • 0034858093 scopus 로고    scopus 로고
    • Reverse transcription of retroviruses and LTR retrotransposons
    • Wilhelm, M., and Wilhelm, F. X. (2001) Reverse transcription of retroviruses and LTR retrotransposons. Cell. Mol. Life Sci. 58, 1246-1262.
    • (2001) Cell. Mol. Life Sci , vol.58 , pp. 1246-1262
    • Wilhelm, M.1    Wilhelm, F.X.2
  • 4
    • 2942525660 scopus 로고    scopus 로고
    • Binding, bending and bonding': Polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus
    • Rausch, J. W., and Le Grice, S. F. (2004) 'Binding, bending and bonding': Polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int. J. Biochem. Cell Biol. 36, 1752-1766.
    • (2004) Int. J. Biochem. Cell Biol , vol.36 , pp. 1752-1766
    • Rausch, J.W.1    Le Grice, S.F.2
  • 5
    • 24044444555 scopus 로고    scopus 로고
    • Interaction of the Ty3 reverse transcriptase thumb subdomain with template-primer
    • Bibillo, A., Lener, D., Tewari, A., and Le Grice, S. F. (2005) Interaction of the Ty3 reverse transcriptase thumb subdomain with template-primer. J. Biol. Chem. 280, 30282-30290.
    • (2005) J. Biol. Chem , vol.280 , pp. 30282-30290
    • Bibillo, A.1    Lener, D.2    Tewari, A.3    Le Grice, S.F.4
  • 8
    • 0032573488 scopus 로고    scopus 로고
    • Structure of a covalently trapped catalytic complex of HIV-I reverse transcriptase: Implications for drug resistance
    • Huang, H. F., Chopra, R., Verdine, G. L., and Harrison, S. C. (1998) Structure of a covalently trapped catalytic complex of HIV-I reverse transcriptase: Implications for drug resistance. Science 282, 1669-1675.
    • (1998) Science , vol.282 , pp. 1669-1675
    • Huang, H.F.1    Chopra, R.2    Verdine, G.L.3    Harrison, S.C.4
  • 9
    • 40749154889 scopus 로고    scopus 로고
    • High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers
    • Yi-Brunozzi, H. Y., Brinson, R. G., Brabazon, D. M., Lener, D., Le Grice, S. F., and Marino, J. P. (2008) High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers. Chem. Biol. 15, 254-262.
    • (2008) Chem. Biol , vol.15 , pp. 254-262
    • Yi-Brunozzi, H.Y.1    Brinson, R.G.2    Brabazon, D.M.3    Lener, D.4    Le Grice, S.F.5    Marino, J.P.6
  • 11
    • 0001681723 scopus 로고
    • Extraction of ions from solution under atmospheric pressure: A method of mass spectometric analysis of bioorganic compounds
    • Aleksandrov, M., Gall, L., Krasnov, V., Nikolaev, V., and Pavlenko, V. (1984) Extraction of ions from solution under atmospheric pressure: A method of mass spectometric analysis of bioorganic compounds. Dokl. Akad. Nauk 277, 379-383.
    • (1984) Dokl. Akad. Nauk , vol.277 , pp. 379-383
    • Aleksandrov, M.1    Gall, L.2    Krasnov, V.3    Nikolaev, V.4    Pavlenko, V.5
  • 12
    • 33748168091 scopus 로고
    • Electrospray Ion-source: Another variation on the free-jet theme
    • Yamashita, M., and Fenn, J. B. (1984) Electrospray Ion-source: Another variation on the free-jet theme. J. Phys. Chem. 88, 4451-4459.
    • (1984) J. Phys. Chem , vol.88 , pp. 4451-4459
    • Yamashita, M.1    Fenn, J.B.2
  • 13
    • 0040295109 scopus 로고
    • Theory of Fourier-transform ion cyclotron resonance mass spectrometry 2. Signal modeling for ioncyclotron resonance
    • Comisarow, M. B. (1978) Theory of Fourier-transform ion cyclotron resonance mass spectrometry 2. Signal modeling for ioncyclotron resonance. J. Chem. Phys. 69, 4097-4104.
    • (1978) J. Chem. Phys , vol.69 , pp. 4097-4104
    • Comisarow, M.B.1
  • 14
    • 0031623267 scopus 로고    scopus 로고
    • Fourier transform ion cyclotron resonance mass spectrometry: A primer
    • Marshall, A. G., Hendrickson, C. L., and Jackson, G. S. (1998) Fourier transform ion cyclotron resonance mass spectrometry: A primer. Mass Spectrom. Rev. 17, 1-35.
    • (1998) Mass Spectrom. Rev , vol.17 , pp. 1-35
    • Marshall, A.G.1    Hendrickson, C.L.2    Jackson, G.S.3
  • 15
    • 33751529972 scopus 로고    scopus 로고
    • Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1
    • Hagan, N. A., and Fabris, D. (2007) Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1. J. Mol. Biol. 365, 396-410.
    • (2007) J. Mol. Biol , vol.365 , pp. 396-410
    • Hagan, N.A.1    Fabris, D.2
  • 16
    • 0042820036 scopus 로고    scopus 로고
    • Direct mass spectrometric determination of the stoichiometry and binding affinity of the complexes between nucleocapsid protein and RNA stem-loop hairpins of the HIV-1 psi-recognition element
    • Hagan, N., and Fabris, D. (2003) Direct mass spectrometric determination of the stoichiometry and binding affinity of the complexes between nucleocapsid protein and RNA stem-loop hairpins of the HIV-1 psi-recognition element. Biochemistry 42, 10736-10745.
    • (2003) Biochemistry , vol.42 , pp. 10736-10745
    • Hagan, N.1    Fabris, D.2
  • 17
    • 33748975408 scopus 로고    scopus 로고
    • Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry
    • Turner, K. B., Hagan, N. A., Kohlway, A. S., and Fabris, D. (2006) Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 17, 1401-1411.
    • (2006) J. Am. Soc. Mass Spectrom , vol.17 , pp. 1401-1411
    • Turner, K.B.1    Hagan, N.A.2    Kohlway, A.S.3    Fabris, D.4
  • 18
    • 33644994792 scopus 로고    scopus 로고
    • Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA
    • Turner, K. B., Hagan, N. A., and Fabris, D. (2006) Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA. Nucleic Acids Res. 34, 1305-1316.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1305-1316
    • Turner, K.B.1    Hagan, N.A.2    Fabris, D.3
  • 19
    • 0001004129 scopus 로고    scopus 로고
    • Mass selection of ions in a Fourier transform ion cyclotron resonance trap using correlated harmonic excitation fields (CHEF)
    • de Koning, L. J., Nibbering, N. M. M., van Orden, S. L., and Laukien, F. H. (1997) Mass selection of ions in a Fourier transform ion cyclotron resonance trap using correlated harmonic excitation fields (CHEF). Int. J. Mass Spectrom. 165, 209-219.
    • (1997) Int. J. Mass Spectrom , vol.165 , pp. 209-219
    • de Koning, L.J.1    Nibbering, N.M.M.2    van Orden, S.L.3    Laukien, F.H.4
  • 20
    • 0025780005 scopus 로고
    • Sustained off-resonance irradiation of collision-activated dissociation involving Fourier transform mass spectrometry: Collision dissociation technique that emulates infrared multiphoton dissociation
    • Gauthier, J. W., Trautman, T. R., and Jacobson, D. B. (1991) Sustained off-resonance irradiation of collision-activated dissociation involving Fourier transform mass spectrometry: Collision dissociation technique that emulates infrared multiphoton dissociation. Anal. Chim. Acta 246, 211-225.
    • (1991) Anal. Chim. Acta , vol.246 , pp. 211-225
    • Gauthier, J.W.1    Trautman, T.R.2    Jacobson, D.B.3
  • 21
    • 0016751670 scopus 로고
    • Evidence for sequence preferences in intercalative binding of ethidium-bromide to dinucleoside monophosphates
    • Krugh, T. R., and Reinhardt, C. G. (1975) Evidence for sequence preferences in intercalative binding of ethidium-bromide to dinucleoside monophosphates. J. Mol. Biol. 97, 133-162.
    • (1975) J. Mol. Biol , vol.97 , pp. 133-162
    • Krugh, T.R.1    Reinhardt, C.G.2
  • 22
    • 0021128830 scopus 로고
    • Ethidium binding sites on plasmidDNAdetermined by photoaffinity labeling
    • Hardwick, J. M., Vonsprecken, R. S., Yielding, K. L., and Yielding, L. W. (1984) Ethidium binding sites on plasmidDNAdetermined by photoaffinity labeling. J. Biol. Chem. 259, 1090-1097.
    • (1984) J. Biol. Chem , vol.259 , pp. 1090-1097
    • Hardwick, J.M.1    Vonsprecken, R.S.2    Yielding, K.L.3    Yielding, L.W.4
  • 25
    • 0019882891 scopus 로고
    • Tandem Mass Spectrometry
    • McLafferty, F.W. (1981) Tandem Mass Spectrometry. Science 214, 280-287.
    • (1981) Science , vol.214 , pp. 280-287
    • McLafferty, F.W.1
  • 26
    • 28444473452 scopus 로고    scopus 로고
    • A ribose sugar conformational switch in the LTR-retrotransposon Ty3 polypurine tract-containing RNA/DNA hybrid
    • Yi-Brunozzi, H. Y., Brabazon, D. M., Lener, D., Le Grice, S. F., and Marino, J. P. (2005) A ribose sugar conformational switch in the LTR-retrotransposon Ty3 polypurine tract-containing RNA/DNA hybrid. J. Am. Chem. Soc. 127, 16344-16345.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 16344-16345
    • Yi-Brunozzi, H.Y.1    Brabazon, D.M.2    Lener, D.3    Le Grice, S.F.4    Marino, J.P.5
  • 27
    • 3343019139 scopus 로고    scopus 로고
    • Drug targeting of HIV-1RNA3DNAhybrid structures: Thermodynamics of recognition and impact on reverse transcriptase-mediated ribonuclease H activity and viral replication
    • Li, T. K., Barbieri, C. M., Lin, H. C., Rabson, A. B., Yang, G., Fan, Y., Gaffney, B. L., Jones, R. A., and Pilch, D. S. (2004) Drug targeting of HIV-1RNA3DNAhybrid structures: Thermodynamics of recognition and impact on reverse transcriptase-mediated ribonuclease H activity and viral replication. Biochemistry 43, 9732-9742.
    • (2004) Biochemistry , vol.43 , pp. 9732-9742
    • Li, T.K.1    Barbieri, C.M.2    Lin, H.C.3    Rabson, A.B.4    Yang, G.5    Fan, Y.6    Gaffney, B.L.7    Jones, R.A.8    Pilch, D.S.9
  • 28
    • 0029932653 scopus 로고    scopus 로고
    • Neomycin, spermine and hexaamminecobalt (III) share common structural motifs in converting B- to A-DNA
    • Robinson, H., and Wang, A. H. (1996) Neomycin, spermine and hexaamminecobalt (III) share common structural motifs in converting B- to A-DNA. Nucleic Acids Res. 24, 676-682.
    • (1996) Nucleic Acids Res , vol.24 , pp. 676-682
    • Robinson, H.1    Wang, A.H.2
  • 29
    • 0041932005 scopus 로고    scopus 로고
    • Aminoglycoside (neomycin) preference is for A-form nucleic acids, not just RNA: Results from a competition dialysis study
    • Arya, D. P., Xue, L., and Willis, B. (2003) Aminoglycoside (neomycin) preference is for A-form nucleic acids, not just RNA: Results from a competition dialysis study. J. Am. Chem. Soc. 125, 10148-10149.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 10148-10149
    • Arya, D.P.1    Xue, L.2    Willis, B.3
  • 30
    • 0029820641 scopus 로고    scopus 로고
    • Comparison of the thermodynamic stabilities and solution conformations of DNA·RNA hybrids containing purine-rich and pyrimidine-rich strands with DNA and RNA duplexes
    • Gyi, J. I., Conn, G. L., Lane, A. N., and Brown, T. (1996) Comparison of the thermodynamic stabilities and solution conformations of DNA·RNA hybrids containing purine-rich and pyrimidine-rich strands with DNA and RNA duplexes. Biochemistry 35, 12538-12548.
    • (1996) Biochemistry , vol.35 , pp. 12538-12548
    • Gyi, J.I.1    Conn, G.L.2    Lane, A.N.3    Brown, T.4
  • 31
    • 3543005385 scopus 로고    scopus 로고
    • Thermodynamics of protein-ligand interactions: History, presence, and future aspects
    • Perozzo, R., Folkers, G., and Scapozza, L. (2004) Thermodynamics of protein-ligand interactions: History, presence, and future aspects. J. Recept. Signal Transduction 24, 1-52.
    • (2004) J. Recept. Signal Transduction , vol.24 , pp. 1-52
    • Perozzo, R.1    Folkers, G.2    Scapozza, L.3
  • 33
    • 12444315624 scopus 로고    scopus 로고
    • Aminoglycoside complexation with a DNA3RNA hybrid duplex: The thermodynamics of recognition and inhibition of RNA processing enzymes
    • Barbieri, C. M., Li, T. K., Guo, S., Wang, G., Shallop, A. J., Pan, W., Yang, G., Gaffney, B. L., Jones, R. A., and Pilch, D. S. (2003) Aminoglycoside complexation with a DNA3RNA hybrid duplex: The thermodynamics of recognition and inhibition of RNA processing enzymes. J. Am. Chem. Soc. 125, 6469-6477.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 6469-6477
    • Barbieri, C.M.1    Li, T.K.2    Guo, S.3    Wang, G.4    Shallop, A.J.5    Pan, W.6    Yang, G.7    Gaffney, B.L.8    Jones, R.A.9    Pilch, D.S.10
  • 34
    • 0037424612 scopus 로고    scopus 로고
    • Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: Elucidation of the number of drug amino groups involved and their identities
    • Kaul, M., Barbieri, C. M., Kerrigan, J. E., and Pilch, D. S. (2003) Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: Elucidation of the number of drug amino groups involved and their identities. J. Mol. Biol. 326, 1373-1387.
    • (2003) J. Mol. Biol , vol.326 , pp. 1373-1387
    • Kaul, M.1    Barbieri, C.M.2    Kerrigan, J.E.3    Pilch, D.S.4
  • 35
    • 7744246534 scopus 로고    scopus 로고
    • Deciphering the origins of observed heat capacity changes for aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA a-sites: A calorimetric, computational, and osmotic stress study
    • Barbieri, C. M., Srinivasan, A. R., and Pilch, D. S. (2004) Deciphering the origins of observed heat capacity changes for aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA a-sites: A calorimetric, computational, and osmotic stress study. J. Am. Chem. Soc. 126, 14380-14388.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 14380-14388
    • Barbieri, C.M.1    Srinivasan, A.R.2    Pilch, D.S.3
  • 36
    • 33646353446 scopus 로고    scopus 로고
    • Examining Ty3 polypurine tract structure and function by nucleoside analog interference
    • Dash, C., Marino, J. P., and Le Grice, S. F. (2006) Examining Ty3 polypurine tract structure and function by nucleoside analog interference. J. Biol. Chem. 281, 2773-2783.
    • (2006) J. Biol. Chem , vol.281 , pp. 2773-2783
    • Dash, C.1    Marino, J.P.2    Le Grice, S.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.