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Volumn 39, Issue 18, 2011, Pages 8148-8162

Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEASE; NUCLEOCAPSID PROTEIN; RNA;

EID: 80054054303     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr526     Document Type: Article
Times cited : (19)

References (69)
  • 2
    • 63049116293 scopus 로고    scopus 로고
    • When is it time for reverse transcription to start and go?
    • Mougel, M., Houzet, L. and Darlix, J.L. (2009) When is it time for reverse transcription to start and go? Retrovirology, 6, 24.
    • (2009) Retrovirology , vol.6 , pp. 24
    • Mougel, M.1    Houzet, L.2    Darlix, J.L.3
  • 3
    • 0023876147 scopus 로고
    • HIV-1 tat trans-activation requires the loop sequence within tar
    • Feng, S. and Holland, E.C. (1988) HIV-1 tat trans-activation requires the loop sequence within tar. Nature, 334, 165-167.
    • (1988) Nature , vol.334 , pp. 165-167
    • Feng, S.1    Holland, E.C.2
  • 4
    • 0028910385 scopus 로고
    • A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses
    • Berkhout, B., Klaver, B. and Das, A.T. (1995) A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses. Virology, 207, 276-281.
    • (1995) Virology , vol.207 , pp. 276-281
    • Berkhout, B.1    Klaver, B.2    Das, A.T.3
  • 7
    • 0034903425 scopus 로고    scopus 로고
    • Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription
    • DOI 10.1017/S1355838201002035
    • Berkhout, B., Vastenhouw, N.L., Klasens, B.I. and Huthoff, H. (2001) Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription. RNA, 7, 1097-1114. (Pubitemid 32726909)
    • (2001) RNA , vol.7 , Issue.8 , pp. 1097-1114
    • Berkhout, B.1    Vastenhouw, N.L.2    Klasens, B.I.F.3    Huthoff, H.4
  • 8
    • 0036298272 scopus 로고    scopus 로고
    • HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence
    • DOI 10.1006/jmbi.2002.5429
    • Bernacchi, S., Stoylov, S., Piemont, E., Ficheux, D., Roques, B.P., Darlix, J.L. and Mely, Y. (2002) HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence. J. Mol. Biol., 317, 385-399. (Pubitemid 34722178)
    • (2002) Journal of Molecular Biology , vol.317 , Issue.3 , pp. 385-399
    • Bernacchi, S.1    Stoylov, S.2    Piemont, E.3    Ficheux, D.4    Roques, B.P.5    Darlix, J.L.6    Mely, Y.7
  • 9
    • 0033856455 scopus 로고    scopus 로고
    • Sequences in the 5' and 3' R elements of human immunodeficiency virus Type 1 critical for efficient reverse transcription
    • DOI 10.1128/JVI.74.18.8324-8334.2000
    • Ohi, Y. and Clever, J.L. (2000) Sequences in the 5' and 3' R elements of human immunodeficiency virus type 1 critical for efficient reverse transcription. J. Virol., 74, 8324-8334. (Pubitemid 30666682)
    • (2000) Journal of Virology , vol.74 , Issue.18 , pp. 8324-8334
    • Ohi, Y.1    Clever, J.L.2
  • 10
    • 0037260333 scopus 로고    scopus 로고
    • Nucleic acid conformational changes essential for HIV-1 nucleocapsid protein-mediated inhibition of self-priming in minus-strand transfer
    • DOI 10.1016/S0022-2836(02)01177-4
    • Hong, M.K., Harbron, E.J., O'Connor, D.B., Guo, J., Barbara, P.F., Levin, J.G. and Musier-Forsyth, K. (2003) Nucleic acid conformational changes essential for HIV-1 nucleocapsid protein-mediated inhibition of self-priming in minus-strand transfer. J. Mol. Biol., 325, 1-10. (Pubitemid 36152994)
    • (2003) Journal of Molecular Biology , vol.325 , Issue.1 , pp. 1-10
    • Hong, M.K.1    Harbron, E.J.2    O'Connor, D.B.3    Guo, J.4    Barbara, P.F.5    Levin, J.G.6    Musier-Forsyth, K.7
  • 11
    • 0037459094 scopus 로고    scopus 로고
    • Destabilization of the HIV-1 complementary sequence of TAR by the nucleocapsid protein through activation of conformational fluctuations
    • DOI 10.1016/S0022-2836(02)01430-4
    • Azoulay, J., Clamme, J.P., Darlix, J.L., Roques, B.P. and Mely, Y. (2003) Destabilization of the HIV-1 complementary sequence of TAR by the nucleocapsid protein through activation of conformational fluctuations. J. Mol. Biol., 326, 691-700. (Pubitemid 36279312)
    • (2003) Journal of Molecular Biology , vol.326 , Issue.3 , pp. 691-700
    • Azoulay, J.1    Clamme, J.-P.2    Darlix, J.-L.3    Roques, B.P.4    Mely, Y.5
  • 14
    • 0028113905 scopus 로고
    • Human immunodeficiency virus nucleocapsid protein accelerates strand transfer of the terminally redundant sequences involved in reverse transcription
    • You, J.C. and McHenry, C.S. (1994) Human immunodeficiency virus nucleocapsid protein accelerates strand transfer of the terminally redundant sequences involved in reverse transcription. J. Biol. Chem., 269, 31491-31495. (Pubitemid 24379506)
    • (1994) Journal of Biological Chemistry , vol.269 , Issue.50 , pp. 31491-31495
    • You, J.C.1    McHenry, C.S.2
  • 16
    • 84937346333 scopus 로고
    • Recombinant HIV-1 nucleocapsid protein accelerates HIV-1 reverse transcriptase catalyzed DNA strand transfer reactions and modulates RNase H activity
    • DOI 10.1021/bi00250a036
    • Peliska, J.A., Balasubramanian, S., Giedroc, D.P. and Benkovic, S.J. (1994) Recombinant HIV-1 nucleocapsid protein accelerates HIV-1 reverse transcriptase catalyzed DNA strand transfer reactions and modulates RNase H activity. Biochemistry, 33, 13817-13823. (Pubitemid 24381946)
    • (1994) Biochemistry , vol.33 , Issue.46 , pp. 13817-13823
    • Peliska, J.A.1    Balasubramanian, S.2    Giedroc, D.P.3    Benkovic, S.J.4
  • 17
    • 0031007620 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR- dependent self-priming from minus-strand strong-stop DNA
    • Guo, J., Henderson, L.E., Bess, J., Kane, B. and Levin, J.G. (1997) Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA. J. Virol., 71, 5178-5188. (Pubitemid 27258190)
    • (1997) Journal of Virology , vol.71 , Issue.7 , pp. 5178-5188
    • Guo, J.1    Henderson, L.E.2    Bess, J.3    Kane, B.4    Levin, J.G.5
  • 18
    • 0141866872 scopus 로고    scopus 로고
    • Steps of the acceptor invasion mechanism for HIV-1 minus strand strong stop transfer
    • DOI 10.1074/jbc.M305700200
    • Chen, Y., Balakrishnan, M., Roques, B.P. and Bambara, R.A. (2003) Steps of the acceptor invasion mechanism for HIV-1 minus strand strong stop transfer. J. Biol. Chem., 278, 38368-38375. (Pubitemid 37221729)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.40 , pp. 38368-38375
    • Chen, Y.1    Balakrishnan, M.2    Roques, B.P.3    Bambara, R.A.4
  • 19
    • 23144448275 scopus 로고    scopus 로고
    • Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein: Critical Role in Reverse Transcription and Molecular Mechanism
    • DOI 10.1016/S0079-6603(05)80006-6, PII S0079660305800066
    • Levin, J.G., Guo, J., Rouzina, I. and Musier-Forsyth, K. (2005) Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. Prog. Nucleic Acid Res. Mol. Biol., 80, 217-286. (Pubitemid 43574891)
    • (2005) Progress in Nucleic Acid Research and Molecular Biology , vol.80 , pp. 217-286
    • Levin, J.G.1    Guo, J.2    Rouzina, I.3    Musier-Forsyth, K.4
  • 20
    • 43049089699 scopus 로고    scopus 로고
    • Nucleocapsid protein function in early infection processes
    • Thomas, J.A. and Gorelick, R.J. (2008) Nucleocapsid protein function in early infection processes. Virus Res., 134, 39-63.
    • (2008) Virus Res. , vol.134 , pp. 39-63
    • Thomas, J.A.1    Gorelick, R.J.2
  • 21
    • 0037453234 scopus 로고    scopus 로고
    • Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7
    • DOI 10.1016/S0022-2836(03)00244-4
    • Beltz, H., Azoulay, J., Bernacchi, S., Clamme, J.P., Ficheux, D., Roques, B., Darlix, J.L. and Mely, Y. (2003) Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7. J. Mol. Biol., 328, 95-108. (Pubitemid 36390283)
    • (2003) Journal of Molecular Biology , vol.328 , Issue.1 , pp. 95-108
    • Beltz, H.1    Azoulay, J.2    Bernacchi, S.3    Clamme, J.-P.4    Ficheux, D.5    Roques, B.6    Darlix, J.-L.7    Mely, Y.8
  • 22
    • 20844463873 scopus 로고    scopus 로고
    • Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis
    • DOI 10.1016/j.jmb.2005.02.042
    • Beltz, H., Clauss, C., Piemont, E., Ficheux, D., Gorelick, R.J., Roques, B., Gabus, C., Darlix, J.L., de Rocquigny, H. and Mely, Y. (2005) Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis. J. Mol. Biol., 348, 1113-1126. (Pubitemid 40602370)
    • (2005) Journal of Molecular Biology , vol.348 , Issue.5 , pp. 1113-1126
    • Beltz, H.1    Clauss, C.2    Piemont, E.3    Ficheux, D.4    Gorelick, R.J.5    Roques, B.6    Gabus, C.7    Darlix, J.-L.8    De Rocquigny, H.9    Mely, Y.10
  • 23
    • 63349103787 scopus 로고    scopus 로고
    • Sensing peptide-oligonucleotide interactions by a two-color fluorescence label: Application to the HIV-1 nucleocapsid protein
    • Shvadchak, V.V., Klymchenko, A.S., de, R.H. and Mely, Y. (2009) Sensing peptide-oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein. Nucleic Acids Res., 37, e25.
    • (2009) Nucleic Acids Res. , vol.37
    • Shvadchak, V.V.1    Klymchenko, A.S.2    De, R.H.3    Mely, Y.4
  • 24
    • 59649130244 scopus 로고    scopus 로고
    • HIV-1 nucleocapsid protein switches the pathway of transactivation response element RNA/DNA annealing from loop-loop "kissing" to "zipper"
    • Vo, M.N., Barany, G., Rouzina, I. and Musier-Forsyth, K. (2009) HIV-1 nucleocapsid protein switches the pathway of transactivation response element RNA/DNA annealing from loop-loop "kissing" to "zipper". J. Mol. Biol., 386, 789-801.
    • (2009) J. Mol. Biol. , vol.386 , pp. 789-801
    • Vo, M.N.1    Barany, G.2    Rouzina, I.3    Musier-Forsyth, K.4
  • 25
    • 27744552000 scopus 로고    scopus 로고
    • Single-molecule FRET studies of important intermediates in the nucleocapsid-protein-chaperoned minus-strand transfer step in HIV-1 reverse transcription
    • DOI 10.1529/biophysj.105.065326
    • Liu, H.W., Cosa, G., Landes, C.F., Zeng, Y., Kovaleski, B.J., Mullen, D.G., Barany, G., Musier-Forsyth, K. and Barbara, P.F. (2005) Single-molecule FRET studies of important intermediates in the nucleocapsid-protein-chaperoned minus-strand transfer step in HIV-1 reverse transcription. Biophys. J., 89, 3470-3479. (Pubitemid 41636101)
    • (2005) Biophysical Journal , vol.89 , Issue.5 , pp. 3470-3479
    • Liu, H.-W.1    Cosa, G.2    Landes, C.F.3    Zeng, Y.4    Kovaleski, B.J.5    Mullen, D.G.6    Barany, G.7    Musier-Forsyth, K.8    Barbara, P.F.9
  • 26
    • 32044464549 scopus 로고    scopus 로고
    • During the early phase of HIV-1 DNA synthesis, nucleocapsid protein directs hybridization of the TAR complementary sequences via the ends of their double-stranded stem
    • DOI 10.1016/j.jmb.2005.12.038, PII S0022283605016098
    • Godet, J., de, R.H., Raja, C., Glasser, N., Ficheux, D., Darlix, J.L. and Mely, Y. (2006) During the early phase of HIV-1 DNA synthesis, nucleocapsid protein directs hybridization of the TAR complementary sequences via the ends of their double-stranded stem. J. Mol. Biol., 356, 1180-1192. (Pubitemid 43199922)
    • (2006) Journal of Molecular Biology , vol.356 , Issue.5 , pp. 1180-1192
    • Godet, J.1    De Rocquigny, H.2    Raja, C.3    Glasser, N.4    Ficheux, D.5    Darlix, J.-L.6    Mely, Y.7
  • 27
    • 0035883822 scopus 로고    scopus 로고
    • The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination
    • Moumen, A., Polomack, L., Roques, B., Buc, H. and Negroni, M. (2001) The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination. Nucleic Acids Res., 29, 3814-3821. (Pubitemid 32916044)
    • (2001) Nucleic Acids Research , vol.29 , Issue.18 , pp. 3814-3821
    • Moumen, A.1    Polomack, L.2    Roques, B.3    Buc, H.4    Negroni, M.5
  • 29
    • 77957219333 scopus 로고
    • Interactions between HIV-1 nucleocapsid protein and viral DNA may have important functions in the viral life cycle
    • Lapadat-Tapolsky, M., de, R.H., Van, G.D., Roques, B., Plasterk, R. and Darlix, J.L. (1993) Interactions between HIV-1 nucleocapsid protein and viral DNA may have important functions in the viral life cycle. Nucleic Acids Res., 21, 831-839. (Pubitemid 23152989)
    • (1993) Nucleic Acids Research , vol.21 , Issue.4 , pp. 831-839
    • Lapadat-Tapolsky, M.1    De Rocquigny, H.2    Van Gent, D.3    Roques, B.4    Plasterk, R.5    Darlix, J.-L.6
  • 30
    • 0034733376 scopus 로고    scopus 로고
    • Characterization of loose and tight dimer forms of avian leukosis virus RNA
    • Polge, E., Darlix, J.L., Paoletti, J. and Fosse, P. (2000) Characterization of loose and tight dimer forms of avian leukosis virus RNA. J. Mol. Biol., 300, 41-56.
    • (2000) J. Mol. Biol. , vol.300 , pp. 41-56
    • Polge, E.1    Darlix, J.L.2    Paoletti, J.3    Fosse, P.4
  • 31
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan, J.F., Groebe, D.R., Witherell, G.W. and Uhlenbeck, O.C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res., 15, 8783-8798.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 32
    • 0030480505 scopus 로고    scopus 로고
    • A short autocomplementary sequence plays an essential role in avian sarcoma-leukosis virus RNA dimerization
    • DOI 10.1021/bi9613786
    • Fosse, P., Motte, N., Roumier, A., Gabus, C., Muriaux, D., Darlix, J.L. and Paoletti, J. (1996) A short autocomplementary sequence plays an essential role in avian sarcoma-leukosis virus RNA dimerization. Biochemistry, 35, 16601-16609. (Pubitemid 27020503)
    • (1996) Biochemistry , vol.35 , Issue.51 , pp. 16601-16609
    • Fosse, P.1    Motte, N.2    Roumier, A.3    Gabus, C.4    Muriaux, D.5    Darlix, J.-L.6    Paoletti, J.7
  • 33
    • 0018846636 scopus 로고
    • Sequencing end-labeled DNA with base-specific chemical cleavages
    • Maxam, A.M. and Gilbert, W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol., 65, 499-560.
    • (1980) Methods Enzymol. , vol.65 , pp. 499-560
    • Maxam, A.M.1    Gilbert, W.2
  • 34
    • 33748769274 scopus 로고    scopus 로고
    • Mechanistic Studies of Mini-TAR RNA/DNA Annealing in the Absence and Presence of HIV-1 Nucleocapsid Protein
    • DOI 10.1016/j.jmb.2006.08.039, PII S0022283606010679
    • Vo, M.N., Barany, G., Rouzina, I. and Musier-Forsyth, K. (2006) Mechanistic studies of mini-TAR RNA/DNA annealing in the absence and presence of HIV-1 nucleocapsid protein. J. Mol. Biol., 363, 244-261. (Pubitemid 44414853)
    • (2006) Journal of Molecular Biology , vol.363 , Issue.1 , pp. 244-261
    • Vo, M.-N.1    Barany, G.2    Rouzina, I.3    Musier-Forsyth, K.4
  • 36
    • 0030019828 scopus 로고    scopus 로고
    • Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation
    • DOI 10.1021/bi951838f
    • Laughrea, M. and Jette, L. (1996) Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation. Biochemistry, 35, 1589-1598. (Pubitemid 26055293)
    • (1996) Biochemistry , vol.35 , Issue.5 , pp. 1589-1598
    • Laughrea, M.1    Jette, L.2
  • 37
    • 34548431022 scopus 로고    scopus 로고
    • Structural Requirements for Nucleocapsid Protein-mediated Dimerization of Avian Leukosis Virus RNA
    • DOI 10.1016/j.jmb.2007.07.026, PII S0022283607009485
    • Ben Ali, M., Chaminade, F., Kanevsky, I., Ennifar, E., Josset, L., Ficheux, D., Darlix, J.L. and Fosse, P. (2007) Structural requirements for nucleocapsid protein-mediated dimerization of avian leukosis virus RNA. J. Mol. Biol., 372, 1082-1096. (Pubitemid 47368353)
    • (2007) Journal of Molecular Biology , vol.372 , Issue.4 , pp. 1082-1096
    • Ali, M.B.1    Chaminade, F.2    Kanevsky, I.3    Ennifar, E.4    Josset, L.5    Ficheux, D.6    Darlix, J.-L.7    Fosse, P.8
  • 38
    • 0037432329 scopus 로고    scopus 로고
    • Elements located upstream and downstream of the major splice donor site influence the ability of HIV-2 leader RNA to dimerize in vitro
    • DOI 10.1021/bi0271190
    • Lanchy, J.M., Rentz, C.A., Ivanovitch, J.D. and Lodmell, J.S. (2003) Elements located upstream and downstream of the major splice donor site influence the ability of HIV-2 leader RNA to dimerize in vitro. Biochemistry, 42, 2634-2642. (Pubitemid 36330617)
    • (2003) Biochemistry , vol.42 , Issue.9 , pp. 2634-2642
    • Lanchy, J.-M.1    Rentz, C.A.2    Ivanovitch, J.D.3    Lodmell, J.S.4
  • 39
    • 0033617287 scopus 로고    scopus 로고
    • DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes
    • Boiziau, C., Dausse, E., Yurchenko, L. and Toulme, J.J. (1999) DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. J. Biol. Chem., 274, 12730-12737.
    • (1999) J. Biol. Chem. , vol.274 , pp. 12730-12737
    • Boiziau, C.1    Dausse, E.2    Yurchenko, L.3    Toulme, J.J.4
  • 40
    • 0034284412 scopus 로고    scopus 로고
    • NMR characterization of a kissing complex formed between the TAR RNA element of HIV-1 and a DNA aptamer
    • Collin, D., van, H.C., Boiziau, C., Toulme, J.J. and Guittet, E. (2000) NMR characterization of a kissing complex formed between the TAR RNA element of HIV-1 and a DNA aptamer. Nucleic Acids Res., 28, 3386-3391. (Pubitemid 30662305)
    • (2000) Nucleic Acids Research , vol.28 , Issue.17 , pp. 3386-3391
    • Collin, D.1    Van Heijenoort, C.2    Boiziau, C.3    Toulme, J.-J.4    Guittet, E.5
  • 41
    • 2942657412 scopus 로고    scopus 로고
    • Dimerization of retroviral RNA genomes: An inseparable pair
    • DOI 10.1038/nrmicro903
    • Paillart, J.C., Shehu-Xhilaga, M., Marquet, R. and Mak, J. (2004) Dimerization of retroviral RNA genomes: an inseparable pair. Nat. Rev. Microbiol., 2, 461-472. (Pubitemid 39200013)
    • (2004) Nature Reviews Microbiology , vol.2 , Issue.6 , pp. 461-472
    • Paillart, J.-C.1    Shehu-Xhilaga, M.2    Marquet, R.3    Mak, J.4
  • 42
    • 0037264483 scopus 로고    scopus 로고
    • Single-strand-specific nucleases
    • DOI 10.1016/S0168-6445(02)00129-8, PII S0168644502001298
    • Desai, N.A. and Shankar, V. (2003) Single-strand-specific nucleases. FEMS Microbiol. Rev., 26, 457-491. (Pubitemid 36183528)
    • (2003) FEMS Microbiology Reviews , vol.26 , Issue.5 , pp. 457-491
    • Desai, N.A.1    Shankar, V.2
  • 43
    • 3042525130 scopus 로고    scopus 로고
    • Mismatch cleavage by single-strand specific nucleases
    • DOI 10.1093/nar/gkh599
    • Till, B.J., Burtner, C., Comai, L. and Henikoff, S. (2004) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res., 32, 2632-2641. (Pubitemid 38854817)
    • (2004) Nucleic Acids Research , vol.32 , Issue.8 , pp. 2632-2641
    • Till, B.J.1    Burtner, C.2    Comai, L.3    Henikoff, S.4
  • 44
    • 34247492103 scopus 로고    scopus 로고
    • Footprinting: A method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands
    • DOI 10.1016/j.ymeth.2007.01.002, PII S1046202307000059, Methods Related to DNA Sequence Recognition
    • Hampshire, A.J., Rusling, D.A., Broughton-Head, V.J. and Fox, K.R. (2007) Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. Methods, 42, 128-140. (Pubitemid 46661910)
    • (2007) Methods , vol.42 , Issue.2 , pp. 128-140
    • Hampshire, A.J.1    Rusling, D.A.2    Broughton-Head, V.J.3    Fox, K.R.4
  • 45
    • 0031194867 scopus 로고    scopus 로고
    • Analysis of open complex formation during RNA polymerase II transcription initiation using heteroduplex templates and potassium permanganate probing
    • DOI 10.1006/meth.1997.0472
    • Holstege, F.C. and Timmers, H.T. (1997) Analysis of open complex formation during RNA polymerase II transcription initiation using heteroduplex templates and potassium permanganate probing. Methods, 12, 203-211. (Pubitemid 27356916)
    • (1997) Methods: A Companion to Methods in Enzymology , vol.12 , Issue.3 , pp. 203-211
    • Holstege, F.C.P.1    Timmers, H.T.M.2
  • 46
    • 0032491380 scopus 로고    scopus 로고
    • DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA
    • DOI 10.1006/jmbi.1998.2129
    • Craig, M.L., Tsodikov, O.V., McQuade, K.L., Schlax, P.E. Jr, Capp, M.W., Saecker, R.M. and Record, M.T. Jr (1998) DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol., 283, 741-756. (Pubitemid 28496966)
    • (1998) Journal of Molecular Biology , vol.283 , Issue.4 , pp. 741-756
    • Craig, M.L.1    Tsodikov, O.V.2    McQuade, K.L.3    Schlax Jr., P.E.4    Capp, M.W.5    Saecker, R.M.6    Record Jr., M.T.7
  • 47
    • 0019332029 scopus 로고
    • Pyrimidine-specific chemical reactions useful for DNA sequencing
    • Rubin, C.M. and Schmid, C.W. (1980) Pyrimidine-specific chemical reactions useful for DNA sequencing. Nucleic Acids Res., 8, 4613-4619.
    • (1980) Nucleic Acids Res. , vol.8 , pp. 4613-4619
    • Rubin, C.M.1    Schmid, C.W.2
  • 48
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • DOI 10.1093/nar/gkg595
    • Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415. (Pubitemid 37442169)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 50
    • 0031935140 scopus 로고    scopus 로고
    • Sequence-specific binding of human immunodeficiency virus type 1 nucleocapsid protein to short oligonucleotides
    • Fisher, R.J., Rein, A., Fivash, M., Urbaneja, M.A., Casas-Finet, J.R., Medaglia, M. and Henderson, L.E. (1998) Sequence-specific binding of human immunodeficiency virus type 1 nucleocapsid protein to short oligonucleotides. J. Virol., 72, 1902-1909. (Pubitemid 28100742)
    • (1998) Journal of Virology , vol.72 , Issue.3 , pp. 1902-1909
    • Fisher, R.J.1    Rein, A.2    Fivash, M.3    Urbaneja, M.A.4    Casas-Finet, J.R.5    Medaglia, M.6    Henderson, L.E.7
  • 51
    • 2242469712 scopus 로고    scopus 로고
    • Structure of the HIV-1 nucleocapsid protein bound to the SL3 ψ-RNA recognition element
    • DOI 10.1126/science.279.5349.384
    • De Guzman, R.N., Wu, Z.R., Stalling, C.C., Pappalardo, L., Borer, P.N. and Summers, M.F. (1998) Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element. Science, 279, 384-388. (Pubitemid 28063374)
    • (1998) Science , vol.279 , Issue.5349 , pp. 384-388
    • De Guzman, R.N.1    Wu, Z.R.2    Stalling, C.C.3    Pappalardo, L.4    Borer, P.N.5    Summers, M.F.6
  • 52
    • 0033593039 scopus 로고    scopus 로고
    • Nucleic acid sequence discrimination by the HIV-1 nucleocapsid protein NCp7: A fluorescence study
    • Vuilleumier, C., Bombarda, E., Morellet, N., Gerard, D., Roques, B.P. and Mely, Y. (1999) Nucleic acid sequence discrimination by the HIV-1 nucleocapsid protein NCp7: a fluorescence study. Biochemistry, 38, 16816-16825.
    • (1999) Biochemistry , vol.38 , pp. 16816-16825
    • Vuilleumier, C.1    Bombarda, E.2    Morellet, N.3    Gerard, D.4    Roques, B.P.5    Mely, Y.6
  • 53
    • 0034636984 scopus 로고    scopus 로고
    • NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition
    • Amarasinghe, G.K., De Guzman, R.N., Turner, R.B., Chancellor, K.J., Wu, Z.R. and Summers, M.F. (2000) NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition. J. Mol. Biol., 301, 491-511.
    • (2000) J. Mol. Biol. , vol.301 , pp. 491-511
    • Amarasinghe, G.K.1    De Guzman, R.N.2    Turner, R.B.3    Chancellor, K.J.4    Wu, Z.R.5    Summers, M.F.6
  • 54
    • 0037161291 scopus 로고    scopus 로고
    • Affinities of packaging domain loops in HIV-1 RNA for the nucleocapsid protein
    • DOI 10.1021/bi016045+
    • Shubsda, M.F., Paoletti, A.C., Hudson, B.S. and Borer, P.N. (2002) Affinities of packaging domain loops in HIV-1 RNA for the nucleocapsid protein. Biochemistry, 41, 5276-5282. (Pubitemid 34411683)
    • (2002) Biochemistry , vol.41 , Issue.16 , pp. 5276-5282
    • Shubsda, M.F.1    Paoletti, A.C.2    Hudson, B.S.3    Borer, P.N.4
  • 55
    • 0037168488 scopus 로고    scopus 로고
    • Affinities of the nucleocapsid protein for variants of SL3 RNA in HIV-1
    • DOI 10.1021/bi026307n
    • Paoletti, A.C., Shubsda, M.F., Hudson, B.S. and Borer, P.N. (2002) Affinities of the nucleocapsid protein for variants of SL3 RNA in HIV-1. Biochemistry, 41, 15423-15428. (Pubitemid 36008154)
    • (2002) Biochemistry , vol.41 , Issue.51 , pp. 15423-15428
    • Paoletti, A.C.1    Shubsda, M.F.2    Hudson, B.S.3    Borer, P.N.4
  • 56
    • 0029044016 scopus 로고
    • Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1
    • Lapadat-Tapolsky, M., Pernelle, C., Borie, C. and Darlix, J.L. (1995) Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1. Nucleic Acids Res., 23, 2434-2441.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 2434-2441
    • Lapadat-Tapolsky, M.1    Pernelle, C.2    Borie, C.3    Darlix, J.L.4
  • 57
    • 0031106649 scopus 로고    scopus 로고
    • Ordered aggregation of ribonucleic acids by the human immunodeficiency virus type 1 nucleocapsid protein
    • Stoylov, S.P., Vuilleumier, C., Stoylova, E., de, R.H., Roques, B.P., Gerard, D. and Mely, Y. (1997) Ordered aggregation of ribonucleic acids by the human immunodeficiency virus type 1 nucleocapsid protein. Biopolymers, 41, 301-312.
    • (1997) Biopolymers , vol.41 , pp. 301-312
    • Stoylov, S.P.1    Vuilleumier, C.2    Stoylova, E.3    De, R.H.4    Roques, B.P.5    Gerard, D.6    Mely, Y.7
  • 58
    • 33750016312 scopus 로고    scopus 로고
    • Rapid Kinetics of Protein-Nucleic Acid Interaction is a Major Component of HIV-1 Nucleocapsid Protein's Nucleic Acid Chaperone Function
    • DOI 10.1016/j.jmb.2006.08.070, PII S0022283606011272
    • Cruceanu, M., Gorelick, R.J., Musier-Forsyth, K., Rouzina, I. and Williams, M.C. (2006) Rapid kinetics of protein-nucleic acid interaction is a major component of HIV-1 nucleocapsid protein's nucleic acid chaperone function. J. Mol. Biol., 363, 867-877. (Pubitemid 44573231)
    • (2006) Journal of Molecular Biology , vol.363 , Issue.5 , pp. 867-877
    • Cruceanu, M.1    Gorelick, R.J.2    Musier-Forsyth, K.3    Rouzina, I.4    Williams, M.C.5
  • 59
    • 0033803461 scopus 로고    scopus 로고
    • Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus-and plus-strand transfer
    • Guo, J., Wu, T., Anderson, J., Kane, B.F., Johnson, D.G., Gorelick, R.J., Henderson, L.E. and Levin, J.G. (2000) Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus-and plus-strand transfer. J. Virol., 74, 8980-8988.
    • (2000) J. Virol. , vol.74 , pp. 8980-8988
    • Guo, J.1    Wu, T.2    Anderson, J.3    Kane, B.F.4    Johnson, D.G.5    Gorelick, R.J.6    Henderson, L.E.7    Levin, J.G.8
  • 61
    • 0041732006 scopus 로고    scopus 로고
    • Differing roles of the N- and C-terminal zinc fingers in human immunodeficiency virus nucleocapsid protein-enhanced nucleic acid annealing
    • DOI 10.1074/jbc.M303819200
    • Heath, M.J., Derebail, S.S., Gorelick, R.J. and DeStefano, J.J. (2003) Differing roles of the N-and C-terminal zinc fingers in human immunodeficiency virus nucleocapsid protein-enhanced nucleic acid annealing. J. Biol. Chem., 278, 30755-30763. (Pubitemid 36994582)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.33 , pp. 30755-30763
    • Heath, M.J.1    Derebail, S.S.2    Gorelick, R.J.3    DeStefano, J.J.4
  • 62
    • 33750046274 scopus 로고    scopus 로고
    • Structure/function mapping of amino acids in the N-terminal zinc finger of the human immunodeficiency virus type 1 nucleocapsid protein: Residues responsible for nucleic acid helix destabilizing activity
    • DOI 10.1021/bi060925c
    • Narayanan, N., Gorelick, R.J. and DeStefano, J.J. (2006) Structure/function mapping of amino acids in the N-terminal zinc finger of the human immunodeficiency virus type 1 nucleocapsid protein: residues responsible for nucleic acid helix destabilizing activity. Biochemistry, 45, 12617-12628. (Pubitemid 44583703)
    • (2006) Biochemistry , vol.45 , Issue.41 , pp. 12617-12628
    • Narayanan, N.1    Gorelick, R.J.2    DeStefano, J.J.3
  • 63
  • 65
    • 64849111662 scopus 로고    scopus 로고
    • Site-specific characterization of HIV-1 nucleocapsid protein binding to oligonucleotides with two binding sites
    • Avilov, S.V., Godet, J., Piemont, E. and Mely, Y. (2009) Site-specific characterization of HIV-1 nucleocapsid protein binding to oligonucleotides with two binding sites. Biochemistry, 48, 2422-2430.
    • (2009) Biochemistry , vol.48 , pp. 2422-2430
    • Avilov, S.V.1    Godet, J.2    Piemont, E.3    Mely, Y.4
  • 66
    • 79956003291 scopus 로고    scopus 로고
    • Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: Role of sugar deoxyriboses in the binding polarity of NC
    • Bazzi, A., Zargarian, L., Chaminade, F., Boudier, C., de, R.H., Rene, B., Mely, Y., Fosse, P. and Mauffret, O. (2011) Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC. Nucleic Acids Res., 39, 3903-3916.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 3903-3916
    • Bazzi, A.1    Zargarian, L.2    Chaminade, F.3    Boudier, C.4    De, R.H.5    Rene, B.6    Mely, Y.7    Fosse, P.8    Mauffret, O.9
  • 67
    • 70350322944 scopus 로고    scopus 로고
    • HIV-1 nucleocapsid protein bends double-stranded nucleic acids
    • Wang, H., Yeh, Y.S. and Barbara, P.F. (2009) HIV-1 nucleocapsid protein bends double-stranded nucleic acids. J. Am. Chem. Soc., 131, 15534-15543.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 15534-15543
    • Wang, H.1    Yeh, Y.S.2    Barbara, P.F.3
  • 68
    • 0025037779 scopus 로고
    • Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states
    • Kalnik, M.W., Norman, D.G., Li, B.F., Swann, P.F. and Patel, D.J. (1990) Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states. J. Biol. Chem., 265, 636-647.
    • (1990) J. Biol. Chem. , vol.265 , pp. 636-647
    • Kalnik, M.W.1    Norman, D.G.2    Li, B.F.3    Swann, P.F.4    Patel, D.J.5
  • 69
    • 78751668182 scopus 로고    scopus 로고
    • Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription
    • Levin, J.G., Mitra, M., Mascarenhas, A. and Musier-Forsyth, K. (2010) Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription. RNA. Biol., 7, 754-774.
    • (2010) RNA. Biol. , vol.7 , pp. 754-774
    • Levin, J.G.1    Mitra, M.2    Mascarenhas, A.3    Musier-Forsyth, K.4


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