메뉴 건너뛰기




Volumn 37, Issue 12, 2009, Pages 4043-4054

Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOCAPSID PROTEIN; PERMANGANATE POTASSIUM; VIRUS DNA;

EID: 67651146625     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp297     Document Type: Article
Times cited : (11)

References (42)
  • 2
    • 23144448275 scopus 로고    scopus 로고
    • Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: Critical role in reverse transcription and molecular mechanism
    • 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., 80, 217-286.
    • (2005) Prog. Nucleic Acid Res. Mol , vol.80 , pp. 217-286
    • Levin, J.G.1    Guo, J.2    Rouzina, I.3    Musier-Forsyth, K.4
  • 3
    • 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
  • 4
    • 0027367521 scopus 로고
    • Trans-activation of the 5′ to 3′ viral DNA strand transfer by nucleocapsid protein during reverse transcription of HIV1 RNA
    • Darlix,J.L., Vincent,A., Gabus,C., de,R.H. and Roques,B. (1993) Trans-activation of the 5′ to 3′ viral DNA strand transfer by nucleocapsid protein during reverse transcription of HIV1 RNA. C. R. Acad. Sci. III, 316, 763-771.
    • (1993) C. R. Acad. Sci. III , vol.316 , pp. 763-771
    • Darlix, J.L.1    Vincent, A.2    Gabus, C.3    de, R.H.4    Roques, B.5
  • 5
    • 0034903425 scopus 로고    scopus 로고
    • Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription
    • 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.
    • (2001) RNA , vol.7 , pp. 1097-1114
    • Berkhout, B.1    Vastenhouw, N.L.2    Klasens, B.I.3    Huthoff, H.4
  • 7
    • 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.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3814-3821
    • Moumen, A.1    Polomack, L.2    Roques, B.3    Buc, H.4    Negroni, M.5
  • 8
    • 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.
    • (1994) J. Biol. Chem , vol.269 , pp. 31491-31495
    • You, J.C.1    McHenry, C.S.2
  • 9
    • 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
    • Godet,J., de Rocquigny,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.
    • (2006) J. Mol. Biol , vol.356 , 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
  • 10
    • 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
    • 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.
    • (2005) Biophys. J , vol.89 , 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
  • 11
    • 34248397617 scopus 로고    scopus 로고
    • Insights on the role of nucleic acid/protein interactions in chaperoned nucleic acid rearrangements of HIV-1 reverse transcription
    • Liu,H.W., Zeng,Y., Landes,C.F., Kim,Y.J., Zhu,Y., Ma,X., Vo,M.N., Musier-Forsyth,K. and Barbara,P.F. (2007) Insights on the role of nucleic acid/protein interactions in chaperoned nucleic acid rearrangements of HIV-1 reverse transcription. Proc. Natl Acad. Sci. USA, 104, 5261-5267.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 5261-5267
    • Liu, H.W.1    Zeng, Y.2    Landes, C.F.3    Kim, Y.J.4    Zhu, Y.5    Ma, X.6    Vo, M.N.7    Musier-Forsyth, K.8    Barbara, P.F.9
  • 12
    • 34547916462 scopus 로고    scopus 로고
    • Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer
    • Zeng,Y., Liu,H.W., Landes,C.F., Kim,Y.J., Ma,X., Zhu,Y., Musier-Forsyth,K. and Barbara,P.F. (2007) Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer. Proc. Natl Acad. Sci. USA, 104, 12651-12656.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 12651-12656
    • Zeng, Y.1    Liu, H.W.2    Landes, C.F.3    Kim, Y.J.4    Ma, X.5    Zhu, Y.6    Musier-Forsyth, K.7    Barbara, P.F.8
  • 13
    • 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
    • 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.
    • (2003) J. Mol. Biol , vol.328 , 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
  • 14
    • 1942457321 scopus 로고    scopus 로고
    • Role of the structure of the top half of HIV-1 cTAR DNA on the nucleic acid destabilizing activity of the nucleocapsid protein NCp7
    • Beltz,H., Piemont,E., Schaub,E., Ficheux,D., Roques,B., Darlix,J.L. and Mely,Y. (2004) Role of the structure of the top half of HIV-1 cTAR DNA on the nucleic acid destabilizing activity of the nucleocapsid protein NCp7. J. Mol. Biol., 338, 711-723.
    • (2004) J. Mol. Biol , vol.338 , pp. 711-723
    • Beltz, H.1    Piemont, E.2    Schaub, E.3    Ficheux, D.4    Roques, B.5    Darlix, J.L.6    Mely, Y.7
  • 15
    • 33748769274 scopus 로고    scopus 로고
    • Mechanistic studies of mini-TAR RNA/DNA annealing in the absence and presence of HIV-1 nucleocapsid protein
    • 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.
    • (2006) J. Mol. Biol , vol.363 , pp. 244-261
    • Vo, M.N.1    Barany, G.2    Rouzina, I.3    Musier-Forsyth, K.4
  • 16
    • 0028864394 scopus 로고
    • The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein
    • Aboul-ela,F., Karn,J. and Varani,G. (1995) The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol., 253, 313-332.
    • (1995) J. Mol. Biol , vol.253 , pp. 313-332
    • Aboul-ela, F.1    Karn, J.2    Varani, G.3
  • 17
  • 18
    • 0027444622 scopus 로고
    • An NMR study of the HIV-1 TAR element hairpin
    • Jaeger,J.A. and Tinoco,I. Jr. (1993) An NMR study of the HIV-1 TAR element hairpin. Biochemistry, 32, 12522-12530.
    • (1993) Biochemistry , vol.32 , pp. 12522-12530
    • Jaeger, J.A.1    Tinoco Jr., I.2
  • 19
    • 0036290269 scopus 로고    scopus 로고
    • Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings
    • Al Hashimi,H.M., Gosser,Y., Gorin,A., Hu,W., Majumdar,A. and Patel,D.J. (2002) Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J. Mol. Biol., 315, 95-102.
    • (2002) J. Mol. Biol , vol.315 , pp. 95-102
    • Al Hashimi, H.M.1    Gosser, Y.2    Gorin, A.3    Hu, W.4    Majumdar, A.5    Patel, D.J.6
  • 20
    • 0028247062 scopus 로고
    • Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: An extraordinarily stable structure resistant to nucleases and heat
    • Hirao,I., Kawai,G., Yoshizawa,S., Nishimura,Y., Ishido,Y., Watanabe,K. and Miura,K. (1994) Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: An extraordinarily stable structure resistant to nucleases and heat. Nucleic Acids Res., 22, 576-582.
    • (1994) Nucleic Acids Res , vol.22 , pp. 576-582
    • Hirao, I.1    Kawai, G.2    Yoshizawa, S.3    Nishimura, Y.4    Ishido, Y.5    Watanabe, K.6    Miura, K.7
  • 21
    • 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
  • 23
    • 0031572279 scopus 로고    scopus 로고
    • The structure of an essential splicing element: Stem loop IIa from yeast U2 snRNA
    • Stallings,S.C. and Moore,P.B. (1997) The structure of an essential splicing element: Stem loop IIa from yeast U2 snRNA. Structure, 5, 1173-1185.
    • (1997) Structure , vol.5 , pp. 1173-1185
    • Stallings, S.C.1    Moore, P.B.2
  • 25
    • 0037264483 scopus 로고    scopus 로고
    • Single-strand-specific nucleases
    • Desai,N.A. and Shankar,V. (2003) Single-strand-specific nucleases. FEMS Microbiol. Rev., 26, 457-491.
    • (2003) FEMS Microbiol. Rev , vol.26 , pp. 457-491
    • Desai, N.A.1    Shankar, V.2
  • 26
    • 34247492103 scopus 로고    scopus 로고
    • Footprinting: A method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands
    • 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.
    • (2007) Methods , vol.42 , pp. 128-140
    • Hampshire, A.J.1    Rusling, D.A.2    Broughton-Head, V.J.3    Fox, K.R.4
  • 27
    • 0031194867 scopus 로고    scopus 로고
    • Analysis of open complex formation during RNA polymerase II transcription initiation using heteroduplex templates and potassium permanganate probing
    • 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.
    • (1997) Methods , vol.12 , pp. 203-211
    • Holstege, F.C.1    Timmers, H.T.2
  • 28
    • 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
    • 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.
    • (1998) J. Mol. Biol , vol.283 , 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
  • 29
    • 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
  • 30
    • 31944446215 scopus 로고    scopus 로고
    • Resolving the motional modes that code for RNA adaptation
    • Zhang,Q., Sun,X., Watt,E.D. and Al Hashimi,H.M. (2006) Resolving the motional modes that code for RNA adaptation. Science, 311, 653-656.
    • (2006) Science , vol.311 , pp. 653-656
    • Zhang, Q.1    Sun, X.2    Watt, E.D.3    Al Hashimi, H.M.4
  • 31
    • 34247185394 scopus 로고    scopus 로고
    • Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: Role in the kissing-duplex structural transition
    • Sun,X., Zhang,Q. and Al Hashimi,H.M. (2007) Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: Role in the kissing-duplex structural transition. Nucleic Acids Res., 35, 1698-1713.
    • (2007) Nucleic Acids Res , vol.35 , pp. 1698-1713
    • Sun, X.1    Zhang, Q.2    Al Hashimi, H.M.3
  • 32
    • 1842578995 scopus 로고    scopus 로고
    • Argininamide binding arrests global motions in HIV-1 TAR RNA: Comparison with Mg2+-induced conformational stabilization
    • Pitt,S.W., Majumdar,A., Serganov,A., Patel,D.J. and Al Hashimi,H.M. (2004) Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization. J. Mol. Biol., 338, 7-16.
    • (2004) J. Mol. Biol , vol.338 , pp. 7-16
    • Pitt, S.W.1    Majumdar, A.2    Serganov, A.3    Patel, D.J.4    Al Hashimi, H.M.5
  • 33
    • 0031591383 scopus 로고    scopus 로고
    • The structure of an RNA 'kissing' hairpin complex of the HIV TAR hairpin loop and its complement
    • Chang,K.Y. and Tinoco,I. Jr. (1997) The structure of an RNA 'kissing' hairpin complex of the HIV TAR hairpin loop and its complement. J. Mol. Biol., 269, 52-66.
    • (1997) J. Mol. Biol , vol.269 , pp. 52-66
    • Chang, K.Y.1    Tinoco Jr., I.2
  • 34
    • 0038206733 scopus 로고    scopus 로고
    • Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings
    • Al Hashimi,H.M., Pitt,S.W., Majumdar,A., Xu,W. and Patel,D.J. (2003) Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings. J. Mol. Biol., 329, 867-873.
    • (2003) J. Mol. Biol , vol.329 , pp. 867-873
    • Al Hashimi, H.M.1    Pitt, S.W.2    Majumdar, A.3    Xu, W.4    Patel, D.J.5
  • 36
    • 0025900996 scopus 로고
    • Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops
    • Peritz,A.E., Kierzek,R., Sugimoto,N. and Turner,D.H. (1991) Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops. Biochemistry, 30 6428-6436.
    • (1991) Biochemistry , vol.30 , pp. 6428-6436
    • Peritz, A.E.1    Kierzek, R.2    Sugimoto, N.3    Turner, D.H.4
  • 37
    • 33947491695 scopus 로고    scopus 로고
    • Molecular dynamics simulation for probing the flexibility of the 35 nucleotide SL1 sequence kissing complex from HIV-1Lai genomic RNA
    • Mazier,S. and Genest,D. (2007) Molecular dynamics simulation for probing the flexibility of the 35 nucleotide SL1 sequence kissing complex from HIV-1Lai genomic RNA. J. Biomol. Struct. Dyn., 24, 471-479.
    • (2007) J. Biomol. Struct. Dyn , vol.24 , pp. 471-479
    • Mazier, S.1    Genest, D.2
  • 38
    • 20344371430 scopus 로고    scopus 로고
    • Structure of the RNA signal essential for translational frameshifting in HIV-1
    • Gaudin,C., Mazauric,M.H., Traikia,M., Guittet,E., Yoshizawa,S. and Fourmy,D. (2005) Structure of the RNA signal essential for translational frameshifting in HIV-1. J. Mol. Biol., 349, 1024-1035.
    • (2005) J. Mol. Biol , vol.349 , pp. 1024-1035
    • Gaudin, C.1    Mazauric, M.H.2    Traikia, M.3    Guittet, E.4    Yoshizawa, S.5    Fourmy, D.6
  • 39
    • 37549017736 scopus 로고    scopus 로고
    • Visualizing spatially correlated dynamics that directs RNA conformational transitions
    • Zhang,Q., Stelzer,A.C., Fisher,C.K. and Al Hashimi,H.M. (2007) Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature, 450, 1263-1267.
    • (2007) Nature , vol.450 , pp. 1263-1267
    • Zhang, Q.1    Stelzer, A.C.2    Fisher, C.K.3    Al Hashimi, H.M.4
  • 40
    • 41449114103 scopus 로고    scopus 로고
    • Solid-state deuterium NMR studies reveal micros-ns motions in the HIV-1 transactivation response RNA recognition site
    • Olsen,G.L., Echodu,D.C., Shajani,Z., Bardaro,M.F., Jr., Varani,G. and Drobny,G.P. (2008) Solid-state deuterium NMR studies reveal micros-ns motions in the HIV-1 transactivation response RNA recognition site. J. Am. Chem. Soc., 130, 2896-2897.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 2896-2897
    • Olsen, G.L.1    Echodu, D.C.2    Shajani, Z.3    Bardaro Jr., M.F.4    Varani, G.5    Drobny, G.P.6
  • 41
    • 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
    • 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.
    • (2002) J. Mol. Biol , vol.317 , 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
  • 42
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.