-
2
-
-
23144448275
-
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
-
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
-
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
-
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
-
6
-
-
18044365239
-
Specific interactions between HIV-1 nucleocapsid protein and the TAR element
-
Kanevsky,I., Chaminade,F., Ficheux,D., Moumen,A., Gorelick,R., Negroni,M., Darlix,J.L. and Fosse,P. (2005) Specific interactions between HIV-1 nucleocapsid protein and the TAR element. J. Mol. Biol. 348, 1059-1077.
-
(2005)
J. Mol. Biol
, vol.348
, pp. 1059-1077
-
-
Kanevsky, I.1
Chaminade, F.2
Ficheux, D.3
Moumen, A.4
Gorelick, R.5
Negroni, M.6
Darlix, J.L.7
Fosse, P.8
-
7
-
-
0035883822
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
0026651395
-
Conformation of the TAR RNA-arginine complex by NMR spectroscopy
-
Puglisi,J.D., Tan,R., Calnan,B.J., Frankel,A.D. and Williamson,J.R. (1992) Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science, 257, 76-80.
-
(1992)
Science
, vol.257
, pp. 76-80
-
-
Puglisi, J.D.1
Tan, R.2
Calnan, B.J.3
Frankel, A.D.4
Williamson, J.R.5
-
18
-
-
0027444622
-
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
-
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
-
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
-
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
-
22
-
-
17144425757
-
Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase
-
Renisio,J.G., Cosquer,S., Cherrak,I., El Antri,S., Mauffret,O. and Fermandjian,S. (2005) Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase. Nucleic Acids Res., 33, 1970-1981.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1970-1981
-
-
Renisio, J.G.1
Cosquer, S.2
Cherrak, I.3
El Antri, S.4
Mauffret, O.5
Fermandjian, S.6
-
23
-
-
0031572279
-
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
-
24
-
-
0013293280
-
The Xplor-NIH NMR molecular structure determination package
-
Schwieters,C.D., Kuszewski,J.J., Tjandra,N. and Clore,G.M. (2003) The Xplor-NIH NMR molecular structure determination package. J. Magn Reson., 160, 65-73.
-
(2003)
J. Magn Reson
, vol.160
, pp. 65-73
-
-
Schwieters, C.D.1
Kuszewski, J.J.2
Tjandra, N.3
Clore, G.M.4
-
25
-
-
0037264483
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
35
-
-
17144423943
-
Specific binding of poly(ADP-ribose) polymerase-1 to cruciform hairpins
-
Potaman,V.N., Shlyakhtenko,L.S., Oussatcheva,E.A., Lyubchenko,Y.L. and Soldatenkov,V.A. (2005) Specific binding of poly(ADP-ribose) polymerase-1 to cruciform hairpins. J. Mol. Biol., 348, 609-615.
-
(2005)
J. Mol. Biol
, vol.348
, pp. 609-615
-
-
Potaman, V.N.1
Shlyakhtenko, L.S.2
Oussatcheva, E.A.3
Lyubchenko, Y.L.4
Soldatenkov, V.A.5
-
36
-
-
0025900996
-
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
-
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
-
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
-
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
-
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
-
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
-
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
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