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Journal of Biomolecular Structure and Dynamics Volume 16, 1999 - Issue 6
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Original Articles

Dimer Initiation Sequence of HIV-1Lai Genomic RNA: NMR Solution Structure of the Extended Duplex

F. Girard Centre de Biophysique Moléculaire, CNRS Rue C. Sadron, 45071, Orléans Cedex 02, Franceaffiliated to Orléans University
,
F. Barbault Centre de Biophysique Moléculaire, CNRS Rue C. Sadron, 45071, Orléans Cedex 02, Franceaffiliated to Orléans University
,
C. Gouyette Laboratoire de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, Paris, 75724, Cedex 15, France
,
T. Huynh-Dinh Laboratoire de Chimie Organique, Institut Pasteur, 28 rue du Docteur Roux, Paris, 75724, Cedex 15, France
,
J. Paoletti Centre de Biophysique Moléculaire, CNRS Rue C. Sadron, 45071, Orléans Cedex 02, Franceaffiliated to Orléans University
&
G. Lancelot Centre de Biophysique Moléculaire, CNRS Rue C. Sadron, 45071, Orléans Cedex 02, Franceaffiliated to Orléans University
Pages 1145-1157 | Received 15 Mar 1999, Published online: 21 May 2012

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Taejin Kim & Bruce A. Shapiro. (2013) The role of salt concentration and magnesium binding in HIV-1 subtype-A and subtype-B kissing loop monomer structures. Journal of Biomolecular Structure and Dynamics 31:5, pages 495-510.
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Sonia Mazier & Daniel Genest. (2007) Molecular Dynamics Simulation for Probing the Flexibility of the 35 Nucleotide SL1 Sequence Kissing Complex from HIV-1Lai Genomic RNA. Journal of Biomolecular Structure and Dynamics 24:5, pages 471-479.
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Florent Barbault, Tam Huynh-Dinh, Jacques Paoletti & Gérard Lancelot. (2002) A new peculiar DNA structure: NMR solution structure of a DNA kissing complex. Journal of Biomolecular Structure and Dynamics 19:4, pages 649-658.
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ThomasL. James, KennethE. Lind, AntonV. Filikov & Anwer Mujeeb. (2000) Three-Dimensional RNA Structure-Based Drug Discovery. Journal of Biomolecular Structure and Dynamics 17:sup1, pages 201-205.
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Articles from other publishers (39)

Robert J. Blakemore, Cleo Burnett, Canessa Swanson, Siarhei Kharytonchyk, Alice Telesnitsky & James B. Munro. (2021) Stability and conformation of the dimeric HIV-1 genomic RNA 5′UTR. Biophysical Journal 120:21, pages 4874-4890.
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Patricia S. Boyd, Janae B. Brown, Joshua D. Brown, Jonathan Catazaro, Issac Chaudry, Pengfei Ding, Xinmei Dong, Jan Marchant, Colin T. O’Hern, Karndeep Singh, Canessa Swanson, Michael F. Summers & Saif Yasin. (2020) NMR Studies of Retroviral Genome Packaging. Viruses 12:10, pages 1115.
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Charles Bou-Nader & Jinwei Zhang. (2020) Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 25:12, pages 2881.
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Kaiming Zhang, Sarah C. Keane, Zhaoming Su, Rossitza N. Irobalieva, Muyuan Chen, Verna Van, Carly A. Sciandra, Jan Marchant, Xiao Heng, Michael F. Schmid, David A. Case, Steven J. Ludtke, Michael F. Summers & Wah Chiu. (2018) Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. Structure 26:3, pages 490-498.e3.
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Louis G. Smith, Jianbo Zhao, David H. Mathews & Douglas H. Turner. (2017) Physics-based all-atom modeling of RNA energetics and structure. Wiley Interdisciplinary Reviews: RNA 8:5, pages e1422.
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Min Ruan, Mahamadou Seydou, Vincent Noel, Benoit Piro, François Maurel & Florent Barbault. (2017) Molecular Dynamics Simulation of a RNA Aptasensor. The Journal of Physical Chemistry B 121:16, pages 4071-4080.
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Marek Havrila, Marie Zgarbová, Petr Jurečka, Pavel Banáš, Miroslav Krepl, Michal Otyepka & Jiří Šponer. (2015) Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. The Journal of Physical Chemistry B 119:49, pages 15176-15190.
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Nilshad Salim, Rajan Lamichhane, Rui Zhao, Tuhina Banerjee, Jane Philip, David Rueda & Andrew L. Feig. (2012) Thermodynamic and Kinetic Analysis of an RNA Kissing Interaction and Its Resolution into an Extended Duplex. Biophysical Journal 102:5, pages 1097-1107.
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Kun Lu, Xiao Heng & Michael F. Summers. (2011) Structural Determinants and Mechanism of HIV-1 Genome Packaging. Journal of Molecular Biology 410:4, pages 609-633.
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Kevin B. Turner, Andrew S. Kohlway, Nathan A. Hagan & Daniele Fabris. (2009) Noncovalent probes for the investigation of structure and dynamics of protein-nucleic acid assemblies: The case of NC-mediated dimerization of genomic RNA in HIV-1. Biopolymers 91:4, pages 283-296.
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Sonia Mazier & Daniel Genest. (2008) Insight into the intrinsic flexibility of the SL1 stem-loop from genomic RNA of HIV-1 as probed by molecular dynamics simulation. Biopolymers 89:3, pages 187-196.
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H. Yu, T. Li, W. Qiao, Q. Chen & Y. Geng. (2007) Guanine tetrad and palindromic sequence play critical roles in the RNA dimerization of bovine foamy virus. Archives of Virology 152:12, pages 2159-2167.
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Kevin B. Turner, Nathan A. Hagan & Daniele Fabris. (2007) Understanding the Isomerization of the HIV-1 Dimerization Initiation Domain by the Nucleocapsid Protein. Journal of Molecular Biology 369:3, pages 812-828.
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Nathan A. Hagan & Daniele Fabris. (2007) Dissecting the Protein–RNA and RNA–RNA Interactions in the Nucleocapsid-mediated Dimerization and Isomerization of HIV-1 Stemloop 1. Journal of Molecular Biology 365:2, pages 396-410.
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Andrew M.L. Lever. 2007. HIV‐1: Molecular Biology and Pathogenesis Viral Mechanisms, Second Edition. HIV‐1: Molecular Biology and Pathogenesis Viral Mechanisms, Second Edition 1 32 .
Nikolai B. Ulyanov, Anwer Mujeeb, Zhihua Du, Marco Tonelli, Tristram G. Parslow & Thomas L. James. (2006) NMR Structure of the Full-length Linear Dimer of Stem-Loop-1 RNA in the HIV-1 Dimer Initiation Site. Journal of Biological Chemistry 281:23, pages 16168-16177.
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Scott K. SilvermanOliver Mayer, Oliver Mayer, Nikolai Windbichler, Herbert Wank & Renée Schroeder. 2006. Nucleic Acid Switches and Sensors. Nucleic Acid Switches and Sensors 75 86 .
Seiki Baba, Ken-ichi Takahashi, Satoko Noguchi, Hiroshi Takaku, Yoshio Koyanagi, Naoki Yamamoto & Gota Kawai. (2005) Solution RNA Structures of the HIV-1 Dimerization Initiation Site in the Kissing-Loop and Extended-Duplex Dimers. The Journal of Biochemistry 138:5, pages 583-592.
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S. Aci, S. Mazier & D. Genest. (2005) Conformational Pathway for the Kissing Complex→Extended Dimer Transition of the SL1 Stem-Loop from Genomic HIV-1 RNA as Monitored by Targeted Molecular Dynamics Techniques. Journal of Molecular Biology 351:3, pages 520-530.
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S. Aci, L. Gangneux, J. Paoletti & D. Genest. (2004) On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV-1 in solution: A molecular dynamics simulation and electrophoresis study. Biopolymers 74:3, pages 177-188.
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Jean-Christophe Paillart, Miranda Shehu-Xhilaga, Roland Marquet & Johnson Mak. (2004) Dimerization of retroviral RNA genomes: an inseparable pair. Nature Reviews Microbiology 2:6, pages 461-472.
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Mihaela-Rita Mihailescu & John P. Marino. (2004) A proton-coupled dynamic conformational switch in the HIV-1 dimerization initiation site kissing complex. Proceedings of the National Academy of Sciences 101:5, pages 1189-1194.
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Rodney S. Russell, Ariel Roldan, Mervi Detorio, Jing Hu, Mark A. Wainberg & Chen Liang. (2003) Effects of a Single Amino Acid Substitution within thep2 Region of Human Immunodeficiency Virus Type 1 on Packagingof Spliced ViralRNA. Journal of Virology 77:24, pages 12986-12995.
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YiQiong Yuan, Deborah J. Kerwood, Andrew C. Paoletti, Michael F. Shubsda & Philip N. Borer. (2003) Stem of SL1 RNA in HIV-1:  Structure and Nucleocapsid Protein Binding for a 1 × 3 Internal Loop , . Biochemistry 42:18, pages 5259-5269.
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Eric Ennifar, Jean-Christophe Paillart, Roland Marquet, Bernard Ehresmann, Chantal Ehresmann, Philippe Dumas & Philippe Walter. (2003) HIV-1 RNA Dimerization Initiation Site Is Structurally Similar to the Ribosomal A Site and Binds Aminoglycoside Antibiotics. Journal of Biological Chemistry 278:4, pages 2723-2730.
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Manuela J. Rist & John P. Marino. (2002) Mechanism of Nucleocapsid Protein Catalyzed Structural Isomerization of the Dimerization Initiation Site of HIV-1. Biochemistry 41:50, pages 14762-14770.
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Annette M. G. Dirac, Hendrik Huthoff, Jørgen Kjems & Ben Berkhout. (2002) Requirements for RNA heterodimerization of the human immunodeficiency virus type 1 (HIV-1) and HIV-2 genomes. Journal of General Virology 83:10, pages 2533-2542.
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Christine Brunel, Roland Marquet, Pascale Romby & Chantal Ehresmann. (2002) RNA loop–loop interactions as dynamic functional motifs. Biochimie 84:9, pages 925-944.
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Jane Greatorex, José Gallego, Gabriele Varani & Andrew Lever. (2002) Structure and Stability of Wild-type and Mutant RNA Internal Loops from the SL-1 Domain of the HIV-1 Packaging Signal. Journal of Molecular Biology 322:3, pages 543-557.
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Hendrik Huthoff & Ben Berkhout. (2002) Multiple Secondary Structure Rearrangements during HIV-1 RNA Dimerization. Biochemistry 41:33, pages 10439-10445.
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Michael F. Shubsda, Andrew C. Paoletti, Bruce S. Hudson & Philip N. Borer. (2002) Affinities of Packaging Domain Loops in HIV-1 RNA for the Nucleocapsid Protein. Biochemistry 41:16, pages 5276-5282.
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Deborah J. Kerwood, Michael J. Cavaluzzi & Philip N. Borer. (2001) Structure of SL4 RNA from the HIV-1 Packaging Signal , . Biochemistry 40:48, pages 14518-14529.
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T. Monie, J. Greatorex & A.M.L. Lever. (2001) Oligonucleotide mapping of the core genomic RNA dimer linkage in human T-cell leukaemia virus type-1. Virus Research 78:1-2, pages 45-56.
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Florent Barbault & Gérard Lancelot. (2001) Le calcul du déplacement chimique, un outil de validation des structures d’acides nucléiques. Comptes Rendus de l'Académie des Sciences - Series IIC - Chemistry 4:10, pages 779-782.
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Ken-ichi Takahashi, Seiki Baba, Yoshio Koyanagi, Naoki Yamamoto, Hiroshi Takaku & Gota Kawai. (2001) Two Basic Regions of NCp7 Are Sufficient for Conformational Conversion of HIV-1 Dimerization Initiation Site from Kissing-loop Dimer to Extended-duplex Dimer. Journal of Biological Chemistry 276:33, pages 31274-31278.
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Ya-Xiong Feng, Sharon P. Moore, David J. Garfinkel & Alan Rein. (2000) The Genomic RNA in Ty1 Virus-Like Particles Is Dimeric. Journal of Virology 74:22, pages 10819-10821.
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Emmanuelle Polge, Jean-Luc Darlix, Jacques Paoletti & Philippe Fossé. (2000) Characterization of loose and tight dimer forms of avian leukosis virus RNA. Journal of Molecular Biology 300:1, pages 41-56.
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Valérie Theilleux‐Delalande, Frédéric Girard, Tam Huynh‐Dinh, Gérard Lancelot & Jacques Paoletti. (2001) The HIV‐1 Lai RNA dimerization . European Journal of Biochemistry 267:9, pages 2711-2719.
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E Ennifar, M Yusupov, P Walter, R Marquet, B Ehresmann, C Ehresmann & P Dumas. (1999) The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges. Structure 7:11, pages 1439-1449.
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