. Varian and . Unity, ont été obtenus à partir d'un échantillon de 600µL d'ADN à 2,7mM en présence de tampon phosphate (10mM, pH 5.7) Pour le dimère stable, l'échantillon a été testé avec différentes concentrations de NaCl (50, 100 et 150mM) Les modélisations moléculaires ont été réalisées sur une station de calcul linux bi-processeurs (à 450MHz et 512Mo de RAM) à l'aide du logiciel CNS version 1.0, Les analyses et représentations des différentes structures ont été réalisées à l'aide des logiciels CURVES (version 5.0) et MOLMOL (version 2K.1)

A. Abragam and A. , Principles of nuclear magnetism, 1961.

C. Adamo and V. Barone, Toward chemical accuracy in the computation of NMR shieldings: the PBE0 model, Chemical Physics Letters, vol.298, issue.1-3, pp.113-122, 1998.
DOI : 10.1016/S0009-2614(98)01201-9

A. Aldovini and R. A. Young, Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus, J Virol, vol.64, pp.1920-1926, 1990.

F. H. Allain, C. C. Gubser, P. W. Howe, K. Nagai, D. Neuhaus et al., Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation, Nature, vol.380, issue.6575, pp.646-50, 1996.
DOI : 10.1038/380646a0

J. F. Allemand, D. Bensimon, R. Lavery, and V. Croquette, Stretched and overwound DNA forms a Pauling-like structure with exposed bases, Proc. Natl, 1998.
DOI : 10.1126/science.270.5242.1653

URL : https://hal.archives-ouvertes.fr/hal-00313418

S. Altschul, F. Thomas, L. M. Shäffer, A. A. Zhang, J. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

A. Amir-aslani, O. Mauffret, F. Sourgen, S. Neplaz, R. G. Maroun et al., The Hairpin Structure of a Topoisomerase II Site DNA Strand Analyzed by Combined NMR and Energy Minimization Methods, Journal of Molecular Biology, vol.263, issue.5, pp.776-88, 1996.
DOI : 10.1006/jmbi.1996.0615

J. A. Anderson, R. J. Teufel, P. D. Yin, and W. S. Hu, Correlated templateswitching events during minus-strand DNA synthesis: a mechanism for high negative interference during retroviral recombination, J Virol, vol.72, pp.1186-94, 1998.

C. R. Astell, M. B. Chow, and D. C. Ward, Sequence analysis of the termini of virion and replicative forms of minute virus of mice DNA suggests a modified rolling hairpin model for autonomous parvovirus DNA replication, J Virol, vol.54, pp.171-178, 1985.

G. Awang and D. Sen, Mode of dimerization of HIV-1 genomic RNA, Biochemistry, vol.32, issue.42, pp.11453-11460, 1993.
DOI : 10.1021/bi00093a024

B. Ban, C. Ramakrishnan, B. Sundaralingam, and M. , A Single 2???-Hydroxyl Group Converts B-DNA to A-DNA, Journal of Molecular Biology, vol.236, issue.1, pp.275-85, 1994.
DOI : 10.1006/jmbi.1994.1134

F. Baudin, R. Marquet, C. Isel, J. L. Darlix, B. Ehresmann et al., Functional Sites in the 5??? Region of Human Immunodeficiency Virus Type 1 RNA Form Defined Structural Domains, Journal of Molecular Biology, vol.229, issue.2, pp.382-97, 1993.
DOI : 10.1006/jmbi.1993.1041

W. Bender and N. Davidson, Mapping of poly(A) sequences in the electron microscope reveals unusual structure of type C oncornavirus RNA molecules, Cell, vol.7, issue.4, pp.595-607, 1976.
DOI : 10.1016/0092-8674(76)90210-5

B. Berkhout, B. B. Essink, and I. Schoneveld, In vitro dimerization of HIV-2 leader RNA in the absence of PuGGAPuA motifs, Faseb J, vol.7, pp.181-188, 1993.

M. Billeter, T. H. Schaumann, W. Braun, and K. Wüthrich, Restrained energy refinement with two different algorithms and force fields of the structure of the ??-amylase inhibitor tendamistat determined by nmr in solution, Biopolymers, vol.170, issue.4-5, pp.695-706, 1990.
DOI : 10.1002/bip.360290404

C. Boiziau, E. Dausse, Y. Ludmila, and J. J. Toulmé, DNA Aptamers Selected Against the HIV-1trans-Activation-responsive RNA Element Form RNA-DNA Kissing Complexes, Journal of Biological Chemistry, vol.274, issue.18, pp.12730-12737, 1999.
DOI : 10.1074/jbc.274.18.12730

B. Bonnet-mathoniere, P. M. Girard, D. Muriaux, and J. Paoletti, Nucleocapsid Protein 10 Activates Dimerization of the RNA of Moloney Murine Leukaemia Virus in vitro, European Journal of Biochemistry, vol.223, issue.1, pp.129-164, 1996.
DOI : 10.1016/0168-9525(91)90048-U

P. N. Borer, L. Pappalardo, D. J. Kerwood, and I. Pelczer, NMR-based structure determination for unlabelled RNA and DNA, Adv Biophys Chem, vol.6, pp.173-216, 1997.

W. Braun and N. Go, Calculation of protein conformations by proton-proton distance constraints, Journal of Molecular Biology, vol.186, issue.3, pp.611-637, 1985.
DOI : 10.1016/0022-2836(85)90134-2

B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan et al., CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, Journal of Computational Chemistry, vol.I, issue.2, pp.187-217, 1983.
DOI : 10.1002/jcc.540040211

A. T. Brünger, X-PLOR : a system for X-ray crystallography and NMR, 1992.

A. T. Brünger, P. D. Adams, G. M. Clore, W. L. De-lano, P. Gros et al., Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination, Acta Crystallographica Section D Biological Crystallography, vol.54, issue.5, pp.905-926, 1998.
DOI : 10.1107/S0907444998003254

A. T. Brunger, P. D. Adams, G. M. Clore, W. L. Delano, P. Gros et al., Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination, Acta Crystallographica Section D Biological Crystallography, vol.54, issue.5, pp.905-926, 1998.
DOI : 10.1107/S0907444998003254

A. T. Brünger and M. Nilges, Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy, Quarterly Reviews of Biophysics, vol.49, issue.01, pp.49-125, 1993.
DOI : 10.1107/S0108767389000437

D. A. Case, The use of chemical shifts and their anisotropies in biomolecular structure determination, Current Opinion in Structural Biology, vol.8, issue.5, pp.624-654, 1998.
DOI : 10.1016/S0959-440X(98)80155-3

D. A. Case, Interpretation of chemical shifts and coupling constants in macromolecules, Current Opinion in Structural Biology, vol.10, issue.2, pp.197-203, 2000.
DOI : 10.1016/S0959-440X(00)00068-3

D. A. Case, D. A. Pearlman, J. W. Caldwell, T. E. Cheatmam, W. S. Ross et al., AMBER 5, 1997.

K. Y. Chang, I. Tinoco, and . Jr, Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome., Proceedings of the National Academy of Sciences, vol.91, issue.18, pp.8705-8714, 1994.
DOI : 10.1073/pnas.91.18.8705

K. Y. Chang, I. Tinoco, and . Jr, The structure of an RNA ???kissing??? hairpin complex of the HIV TAR hairpin loop and its complement, Journal of Molecular Biology, vol.269, issue.1, pp.52-66, 1997.
DOI : 10.1006/jmbi.1997.1021

T. E. Cheatham, . Iii, and P. A. Kollman, Molecular Dynamics Simulations Highlight the Structural Differences among DNA:DNA, RNA:RNA, and DNA:RNA Hybrid Duplexes, Journal of the American Chemical Society, vol.119, issue.21, pp.4805-4825, 1997.
DOI : 10.1021/ja963641w

F. Clavel and J. M. Orenstein, A mutant of human immunodeficiency virus with reduced RNA packaging and abnormal particle morphology, J Virol, vol.64, pp.5230-5234, 1990.

J. Clever, C. Sassetti, and T. G. Parslow, RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1, J Virol, vol.69, pp.2101-2110, 1995.

J. L. Clever, M. L. Wong, and T. G. Parslow, Requirements for kissing-loopmediated dimerization of human immunodeficiency virus RNA, J Virol, vol.70, pp.5902-5910, 1996.

G. M. Clore, M. R. Starich, and A. M. Gronenborn, Measurement of Residual Dipolar Couplings of Macromolecules Aligned in the Nematic Phase of a Colloidal Suspension of Rod-Shaped Viruses, Journal of the American Chemical Society, vol.120, issue.40, pp.10571-10573, 1998.
DOI : 10.1021/ja982592f

J. M. Coffin, RNA tumor viruses in, Cold Spring Harbor, pp.261-368, 1984.

D. Collin, C. V. Heijenoort, C. Boiziau, J. J. Toulmé, and E. Guittet, NMR characterization of a kissing complex formed between the TAR RNA element of HIV-1 and a DNA aptamer, Nucleic Acids Research, vol.28, issue.17, pp.3386-91, 2000.
DOI : 10.1093/nar/28.17.3386

J. C. Connolly, L. A. Kirkham, and D. R. Leach, The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA, Proceedings of the National Academy of Sciences, vol.350, issue.1, pp.7969-74, 1998.
DOI : 10.1016/S0092-8674(00)80524-3

J. A. Cromsigt, J. Schleucher, K. Kidd-ljubggren, and S. S. Wijmenga, Synthesis of Specifically Deuterated Nucleotides for NMR Studies on RNA, Journal of Biomolecular Structure and Dynamics, vol.116, issue.sup1, pp.211-230, 2000.
DOI : 10.1006/jmre.1997.1286

D. Dam, E. Pleij, K. Draper, and D. , Structural and functional aspects of RNA pseudoknots, Biochemistry, vol.31, pp.11665-76, 1992.

F. Dardel, R. Marquet, C. Ehresmann, B. Ehresmann, and S. Blanquet, Solution studies of the dimerization initiation site of HIV-1 genomic RNA, Nucleic Acids Research, vol.26, issue.15, pp.3567-71, 1998.
DOI : 10.1093/nar/26.15.3567

J. L. Darlix, C. Gabus, M. T. Nugeyre, F. Clavel, and F. Barre-sinoussi, Cis elements and Trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1, Journal of Molecular Biology, vol.216, issue.3, pp.689-99, 1990.
DOI : 10.1016/0022-2836(90)90392-Y

A. C. De-dios, J. L. Roach, and A. E. Walling, The NMR Chemical Shift: Local Geometry Effects, Modelling NMR chemical shifts. Gaining insights into structure and environment, pp.220-239, 1999.
DOI : 10.1021/bk-1999-0732.ch016

H. De-rocquigny, C. Gabus, A. Vincent, M. C. Fournie-zaluski, B. Roques et al., Viral RNA annealing activities of human immunodeficiency virus type 1 nucleocapsid protein require only peptide domains outside the zinc fingers., Proceedings of the National Academy of Sciences, vol.89, issue.14, pp.6472-6478, 1992.
DOI : 10.1073/pnas.89.14.6472

F. Delaglio, G. Kontaxis, and A. Bax, Protein Structure Determination Using Molecular Fragment Replacement and NMR Dipolar Couplings, Journal of the American Chemical Society, vol.122, issue.9, pp.2142-2145, 2000.
DOI : 10.1021/ja993603n

M. Delepierre, J. Igolen, and B. P. Roques, Study of the bisintercalation of the antitumor drug ditercalinium by31P-nmr, Biopolymers, vol.73, issue.6, pp.957-68, 1988.
DOI : 10.1002/bip.360270606

T. Dieckmann, E. Suzuki, G. K. Nakamura, and J. Feigon, Solution structure of an ATP-binding RNA aptamer reveals a novel fold, Rna, vol.2, pp.628-668, 1996.

E. Amri, C. Mauffret, O. Monnot, M. Tevanian, G. Lescot et al., A DNA hairpin with a single residue loop closed by a strongly distorted watson-crick G??C base-pair, Journal of Molecular Biology, vol.294, issue.2, pp.427-469, 1999.
DOI : 10.1006/jmbi.1999.3270

URL : https://hal.archives-ouvertes.fr/hal-00284928

E. Ennifar, M. Yusupov, P. Walter, R. Marquet, B. Ehresmann et al., The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges, Structure, vol.7, issue.11, pp.1439-1488, 1999.
DOI : 10.1016/S0969-2126(00)80033-7

A. D. Frankel and J. A. Young, HIV-1: Fifteen Proteins and an RNA, Annual Review of Biochemistry, vol.67, issue.1, pp.1-25, 1998.
DOI : 10.1146/annurev.biochem.67.1.1

K. Gehring, J. L. Leroy, and M. Guéron, A tetrameric DNA structure with protonated cytosine-cytosine base pairs, Nature, vol.363, issue.6429, pp.561-566, 1993.
DOI : 10.1038/363561a0

R. F. Gesteland, T. R. Cech, and J. F. Atkins, The RNA world, second edition, 1998.

C. Giessner-prettre and B. Pullman, Quantum mechanical calculations of NMR chemical shifts in nucleic acids, Quarterly Reviews of Biophysics, vol.2, issue.3-4, pp.113-72, 1987.
DOI : 10.1038/311584a0

F. Girard, Etude par RMN de la structure des dimères de la séquence d'ARN SL1- 23mer initiant la dimérisation chez VIH-1Lai, Thèse de doctorat, 2000.

F. Girard, F. Barbault, C. Gouyette, T. Huynh-dinh, J. Paoletti et al., Genomic RNA: NMR Solution Structure of the Extended Duplex, Journal of Biomolecular Structure and Dynamics, vol.217, issue.6, pp.1145-57, 1999.
DOI : 10.1006/jmbi.1997.1096

C. Glemarec, J. Kufel, A. Foldesi, T. Maltseva, A. Sandstrom et al., The NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non-uniformly deuterium labelled counterpart [the 'NMR- window' concept], Nucleic Acids Research, vol.24, issue.11, pp.2022-2057, 1996.
DOI : 10.1093/nar/24.11.2022

D. G. Gorenstein, Phosphorus 31 NMR, Principles and applications, 1984.

K. L. Greene, Y. Wang, and D. Live, Influence of the glycosidic torsion angle on 13C and 15N shifts in guanosine nucleotides: Investigations of G-tetrad models with alternating syn and anti bases, Journal of Biomolecular NMR, vol.5, issue.4, pp.333-341, 1995.
DOI : 10.1007/BF00182274

C. C. Gubser and G. Varani, Structure of the Polyadenylation Regulatory Element of the Human U1A Pre-mRNA 3???-Untranslated Region and Interaction with the U1A Protein, Biochemistry, vol.35, issue.7, pp.2253-67, 1996.
DOI : 10.1021/bi952319f

P. Güntert, Structure calculation of biological macromolecules from NMR data, Quarterly Reviews of Biophysics, vol.31, issue.2, pp.145-237, 1998.
DOI : 10.1017/S0033583598003436

P. Guntert, W. Braun, and K. Wuthrich, Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA, Journal of Molecular Biology, vol.217, issue.3, pp.517-547, 1991.
DOI : 10.1016/0022-2836(91)90754-T

P. Guntert, Y. Q. Qian, G. Otting, M. Muller, W. Gehring et al., Structure determination of the Antp(C39 ??? S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA, Journal of Molecular Biology, vol.217, issue.3, pp.531-571, 1991.
DOI : 10.1016/0022-2836(91)90755-U

K. Hall, P. Cruz, I. Tinoco, . Jr, T. M. Jovin et al., ???Z-RNA??????a left-handed RNA double helix, Nature, vol.106, issue.5986, pp.584-590, 1984.
DOI : 10.1038/311584a0

T. F. Havel and K. Wuthrich, An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution, Journal of Molecular Biology, vol.182, issue.2, pp.281-94, 1985.
DOI : 10.1016/0022-2836(85)90346-8

C. Helene, The anti-gene strategy: control of gene expression by triplex-formingoligonucleotides, Anticancer Drug Des, vol.6, pp.569-84, 1991.

T. Helgaker, M. Jaszunski, and K. Ruud, Ab Initio Methods for the Calculation of NMR Shielding and Indirect Spin???Spin Coupling Constants, Chemical Reviews, vol.99, issue.1, pp.293-352, 1999.
DOI : 10.1021/cr960017t

T. Hermann and D. J. Patel, RNA bulges as architectural and recognition motifs, Structure, vol.8, issue.3, pp.47-54, 2000.
DOI : 10.1016/S0969-2126(00)00110-6

I. Hirao, Y. Nishimura, T. Naraoka, K. Watanabe, and K. Miura, Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC), Nucleic Acids Research, vol.17, issue.6, pp.2223-2254, 1989.
DOI : 10.1093/nar/17.6.2223

I. Hirao, Y. Nishimura, Y. Tagawa, K. Watanabe, and K. Miura, Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCFAAAGC)and their effect on DNA sequencing, Nucleic Acids Research, vol.20, issue.15, pp.3891-3897, 1992.
DOI : 10.1093/nar/20.15.3891

J. A. Ippolito and T. A. Steitz, A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation, Proceedings of the National Academy of Sciences, vol.65, issue.10, pp.9819-9843, 1998.
DOI : 10.1126/science.252.5009.1167

T. L. James, [14] Assessment of quality of derived macromolecular structures, Methods Enzymol, vol.239, pp.416-455, 1994.
DOI : 10.1016/S0076-6879(94)39016-9

T. L. James, Computational strategies pertinent to NMR solution structure determination, Current Opinion in Structural Biology, vol.4, issue.2, pp.275-84, 1994.
DOI : 10.1016/S0959-440X(94)90320-4

F. Jiang, R. A. Kumar, R. A. Jones, and D. J. Patel, Structural basis of RNA folding and recognition in an AMP???RNA aptamer complex, Nature, vol.382, issue.6587, pp.183-189, 1996.
DOI : 10.1038/382183a0

J. S. Jones, R. W. Allan, and H. M. Temin, One retroviral RNA is sufficient for synthesis of viral DNA, J Virol, vol.68, pp.207-223, 1994.

F. M. Jucker, H. A. Heus, P. F. Yip, E. H. Moors, and A. Pardi, A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops, Journal of Molecular Biology, vol.264, issue.5, pp.968-80, 1996.
DOI : 10.1006/jmbi.1996.0690

M. W. Kalnik, D. G. Norman, P. F. Swann, and D. J. Patel, Conformation of adenosine bulge-containing deoxytridecanucleotide duplexes in solution. Extra adenosine stacks into duplex independent of flanking sequence and temperature, J Biol Chem, vol.264, pp.3702-3714, 1989.

M. Karplus, Contact Electron???Spin Coupling of Nuclear Magnetic Moments, The Journal of Chemical Physics, vol.30, issue.1, pp.11-16, 1959.
DOI : 10.1063/1.1729860

R. A. Katz, K. Gravuer, and A. M. Skalka, A Preferred Target DNA Structure for Retroviral Integrasein Vitro, Journal of Biological Chemistry, vol.273, issue.37, pp.24190-24195, 1998.
DOI : 10.1074/jbc.273.37.24190

B. Kemper and E. Janz, Function of gene 49 of bacteriophage T4. I. Isolation and biochemical characterization of very fast-sedimenting DNA, J Virol, vol.18, pp.992-1001, 1976.

C. H. Kim, I. Tinoco, and . Jr, A retroviral RNA kissing complex containing only two G{middle dot}C base pairs, Proceedings of the National Academy of Sciences, vol.60, issue.1, pp.9396-401, 2000.
DOI : 10.1146/annurev.bi.60.070191.003215

S. G. Kim, L. J. Lin, and B. R. Reid, Determination of nucleic acid backbone conformation by proton NMR, Biochemistry, vol.31, issue.14, pp.3564-74, 1992.
DOI : 10.1021/bi00129a003

S. H. Kim, F. L. Suddath, G. J. Quigley, A. Mcpherson, J. L. Sussman et al., Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA, Science, vol.185, issue.4149, pp.435-475, 1974.
DOI : 10.1126/science.185.4149.435

S. Kirkpatrick, C. D. Gelatt, and M. P. Vecchi, Optimization by Simulated Annealing, Science, vol.220, issue.4598, pp.671-80, 1983.
DOI : 10.1126/science.220.4598.671

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

M. H. Kolk, M. Van-der-graaf, S. S. Wijmenga, C. W. Pleij, H. A. Heus et al., NMR Structure of a Classical Pseudoknot: Interplay of Single- and Double-Stranded RNA, Science, vol.280, issue.5362, pp.434-442, 1998.
DOI : 10.1126/science.280.5362.434

J. Kuszewski, A. M. Gronenborn, and G. M. Clore, The Impact of Direct Refinement against Proton Chemical Shifts on Protein Structure Determination by NMR, Journal of Magnetic Resonance, Series B, vol.107, issue.3, pp.293-300, 1995.
DOI : 10.1006/jmrb.1995.1093

J. Kuszewski, A. M. Gronenborn, and G. M. Clore, A Potential Involving Multiple Proton Chemical-Shift Restraints for Nonstereospecifically Assigned Methyl and Methylene Protons, Journal of Magnetic Resonance, Series B, vol.112, issue.1, pp.79-81, 1996.
DOI : 10.1006/jmrb.1996.0113

J. Kuszewski, J. Qin, A. M. Gronenborn, and G. M. Clore, The Impact of Direct Refinement against 13C?? and 13C?? Chemical Shifts on Protein Structure Determination by NMR, Journal of Magnetic Resonance, Series B, vol.106, issue.1, pp.92-98, 1995.
DOI : 10.1006/jmrb.1995.1017

L. Lacroix, H. Liénard, E. Labourier, M. Djavaheri-mergny, J. Lacoste et al., Identification of two human nuclear proteins that recognise the cytosine-rich strand of human telomeres in vitro, Nucleic Acids Research, vol.28, issue.7, pp.1564-75, 2000.
DOI : 10.1093/nar/28.7.1564

G. Lancelot, J. L. Guesnet, and F. Vovelle, Solution structure of the parallel-stranded duplex oligonucleotide .alpha.-d(TCTAAAC)-.beta.-(AGATTTG) via complete relaxation matrix analysis of the NOE effects and molecular mechanics calculations, Biochemistry, vol.28, issue.19, pp.7871-7879, 1989.
DOI : 10.1021/bi00445a049

M. Laughrea and L. Jette, A 19-Nucleotide Sequence Upstream of the 5' Major Splice Donor Is Part of the Dimerization Domain of Human Immunodeficiency Virus 1 Genomic RNA, Biochemistry, vol.33, issue.45, pp.13464-74, 1994.
DOI : 10.1021/bi00249a035

R. Lavery and H. Sklenar, The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids, Journal of Biomolecular Structure and Dynamics, vol.328, issue.1, pp.63-91, 1988.
DOI : 10.1016/0022-2836(78)90209-7

URL : https://hal.archives-ouvertes.fr/hal-00313457

R. Lavery and H. Sklenar, Defining the Structure of Irregular Nucleic Acids: Conventions and Principles, Journal of Biomolecular Structure and Dynamics, vol.138, issue.4, pp.655-67, 1989.
DOI : 10.1016/0079-6107(70)90027-1

URL : https://hal.archives-ouvertes.fr/hal-00313452

R. Lavery and H. Sklenar, A quantitative description of conformation of biological macromolecules, 1990.

R. Lavery, K. Zakrzewska, and H. Sklenar, JUMNA (junction minimisation of nucleic acids), Computer Physics Communications, vol.91, issue.1-3, pp.255-62, 1995.
DOI : 10.1016/0010-4655(95)00046-I

A. J. Lee and D. M. Crothers, The solution structure of an RNA loop???loop complex: the ColE1 inverted loop sequence, Structure, vol.6, issue.8, pp.993-1005, 1998.
DOI : 10.1016/S0969-2126(98)00101-4

J. L. Leroy, K. Gehring, A. Kettani, and M. Guéron, Acid multimers of oligodeoxycytodine strands: stoechimoetry, base-pair characterization, and proton exchange properties, Biochemistry, vol.32, pp.4634-4674, 1993.

A. Lever, H. Gottlinger, W. Haseltine, and J. Sodroski, Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions, J Virol, vol.63, pp.4085-4092, 1989.

Y. Liu, D. Zhao, R. Altman, and O. Jardetzky, A systematic comparison of three structure determination methods from NMR data: Dependence upon quality and quantity of data, Journal of Biomolecular NMR, vol.169, issue.4, pp.373-88, 1992.
DOI : 10.1007/BF01874815

S. J. Lodmell, J. C. Paillart, D. Mignot, B. Ehresmann, C. Ehresmann et al., Oligonucleotide-Mediated Inhibition of Genomic RNA Dimerization of HIV-1 Strains MAL and LAI: A Comparative Analysis, Antisense and Nucleic Acid Drug Development, vol.8, issue.6, pp.517-546, 1998.
DOI : 10.1089/oli.1.1998.8.517

J. P. Marino, R. S. Gregorian, . Jr, G. Csankovszki, and D. M. Crothers, Bent helix formation between RNA hairpins with complementary loops, Science, vol.268, issue.5216, pp.1448-54, 1995.
DOI : 10.1126/science.7539549

D. Marion, M. Ikura, R. Tschudin, and A. Bax, Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins, Journal of Magnetic Resonance (1969), vol.85, issue.2, pp.393-402, 1989.
DOI : 10.1016/0022-2364(89)90152-2

R. Marquet, F. Baudin, C. Gabus, J. L. Darlix, M. Mougel et al., Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism, Nucleic Acids Research, vol.19, issue.9, pp.2349-57, 1991.
DOI : 10.1093/nar/19.9.2349

J. A. Mccammon, B. R. Gelin, and M. Karplus, Dynamics of folded proteins, Nature, vol.58, issue.5612, pp.585-90, 1977.
DOI : 10.1038/267585a0

H. Mizuno and M. Sundaralingam, Stacking of Crick Wobble pair and Watson-Crick pair: stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon-anticodon Wobble interaction, Nucleic Acids Research, vol.5, issue.11, pp.4451-61, 1978.
DOI : 10.1093/nar/5.11.4451

M. Mougel, N. Tounekti, J. L. Darlix, J. Paoletti, B. Ehresmann et al., Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization, Nucleic Acids Research, vol.21, issue.20, pp.4677-84, 1993.
DOI : 10.1093/nar/21.20.4677

A. Mujeeb, J. L. Clever, T. M. Billeci, T. L. James, and T. G. Parslow, Structure of the dimer a initiation complex of HIV-1 genomic RNA, Nature Structural Biology, vol.24, issue.6, pp.432-438, 1998.
DOI : 10.1006/jmbi.1997.1284

A. Mujeeb, S. M. Kerwin, G. L. Kenyon, and T. L. James, Solution structure of a conserved DNA sequence from the HIV-1 genome: Restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra, Biochemistry, vol.32, issue.49, pp.13419-13450, 1993.
DOI : 10.1021/bi00212a007

A. Mujeeb, T. G. Parslow, A. Zarrinpar, C. Das, and T. L. James, NMR structure of the mature dimer initiation complex of HIV-1 genomic RNA, FEBS Letters, vol.1, issue.3, pp.387-92, 1999.
DOI : 10.1016/S0014-5793(99)01183-7

D. Muriaux, P. M. Girard, B. Bonnet-mathoniere, and J. Paoletti, Dimerization of HIV-1Lai RNA at Low Ionic Strength: AN AUTOCOMPLEMENTARY SEQUENCE IN THE 5' LEADER REGION IS EVIDENCED BY AN ANTISENSE OLIGONUCLEOTIDE, Journal of Biological Chemistry, vol.270, issue.14, pp.8209-8225, 1995.
DOI : 10.1074/jbc.270.14.8209

K. G. Murti, M. Bondurant, and A. Tereba, Secondary structural features in the 70S RNAs of Moloney murine leukemia and Rous sarcoma viruses as observed by electron microscopy, J Virol, vol.37, pp.411-430, 1981.

S. Neidle, Oxford handbook of nucleic acid structure, 1999.

E. P. Nikonowicz, K. Kalurachchi, and E. Dejong, N labeled RNA oligonucleotide with selective protonation at C5 and C8, FEBS Letters, vol.4, issue.1, pp.109-122, 1997.
DOI : 10.1016/S0014-5793(97)01034-X

E. P. Nikonowicz, M. Michnicka, K. Kalurachchi, and E. Dejong, Preparation and characterization of a uniformly 2 H/ 15 N-labeled RNA oligonucleotide for NMR studies, Nucleic Acids Research, vol.25, issue.7, pp.1390-1396, 1997.
DOI : 10.1093/nar/25.7.1390

M. Nilges, A calculation strategy for the structure determination of symmetric demers by1H NMR, Proteins: Structure, Function, and Genetics, vol.24, issue.3, pp.297-309, 1993.
DOI : 10.1002/prot.340170307

M. Nilges, Structure calculation from NMR data, Current Opinion in Structural Biology, vol.6, issue.5, pp.617-640, 1996.
DOI : 10.1016/S0959-440X(96)80027-3

M. Nilges, G. M. Clore, and A. M. Gronenborn, Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms Circumventing problems associated with folding, FEBS Letters, vol.201, issue.1, pp.129-165, 1988.
DOI : 10.1016/0014-5793(88)80559-3

M. Nilges, G. M. Clore, and A. M. Gronenborn, Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations, FEBS Letters, vol.4, issue.2, pp.317-341, 1988.
DOI : 10.1016/0014-5793(88)81148-7

L. Nilsson and M. Karplus, Empirical energy functions for energy minimization and dynamics of nucleic acids, Journal of Computational Chemistry, vol.18, issue.5, pp.591-616, 1986.
DOI : 10.1002/jcc.540070502

S. Ohki and M. Kainosho, [New aspects is stable-isotope-assisted NMR techniques: application to be structural analysis of larger complexes between proteins and nucleic acids], Tanpakushitsu Kakusan Koso, vol.44, pp.574-81, 1999.

M. Orita, F. Nishikawa, T. Shimayama, K. Taira, Y. Endo et al., High-resolution NMR study of a synthetic oligoribonucleotide with a tetranucleotide GAGA loop that is a substrate for the cytotoxic protein, ricin, Nucleic Acids Research, vol.21, issue.24, pp.5670-5678, 1993.
DOI : 10.1093/nar/21.24.5670

J. C. Paillart, R. Marquet, E. Skripkin, C. Ehresmann, and B. Ehresmann, Dimerization of retroviral genomic RNAs: structural and functional implications, Biochimie, vol.78, issue.7, pp.639-53, 1996.
DOI : 10.1016/S0300-9084(96)80010-1

J. C. Paillart, E. Westhof, C. Ehresmann, B. Ehresmann, and R. Marquet, Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA, Journal of Molecular Biology, vol.270, issue.1, pp.36-49, 1997.
DOI : 10.1006/jmbi.1997.1096

A. Pardi, D. R. Hare, and C. Wang, Determination of DNA structures by NMR and distance geometry techniques: a computer simulation., Proceedings of the National Academy of Sciences, vol.85, issue.23, pp.8785-8794, 1988.
DOI : 10.1073/pnas.85.23.8785

G. N. Pavlakis, The molecular biology of human immunodeficiency virus type 1 in AIDS: biology, diagnosis, treatment and prevention, 1996.

J. P. Perreault, D. Labuda, N. Usman, J. H. Yang, and R. Cedergren, Relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: a model for ribozyme catalysis, Biochemistry, vol.30, issue.16, pp.4020-4025, 1991.
DOI : 10.1021/bi00230a029

K. Pervushin, R. Riek, G. Wider, and K. Wuthrich, Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution, Proceedings of the National Academy of Sciences, vol.40, issue.6, pp.12366-71, 1997.
DOI : 10.1007/BF02192855

M. Piotto, V. Saudek, and V. Sklenar, Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions, Journal of Biomolecular NMR, vol.87, issue.6, pp.661-666, 1992.
DOI : 10.1007/BF02192855

P. Plateau and M. Guéron, Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequences, Journal of the American Chemical Society, vol.104, issue.25, pp.7310-7321, 1982.
DOI : 10.1021/ja00389a067

J. Plavec, C. Thibaudeau, and J. Chattopadhyaya, How Does the 2'-Hydroxy Group Drive the Pseudorotational Equilibrium in Nucleoside and Nucleotide by the Tuning of the 3'-Gauche Effect?, Journal of the American Chemical Society, vol.116, issue.15, pp.6558-65560, 1994.
DOI : 10.1021/ja00094a009

C. W. Pleij, Structure and function of RNA pseudoknots, Genet Eng, vol.17, pp.67-80, 1995.

H. W. Pley, K. M. Flaherty, and D. B. Mckay, Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix, Nature, vol.372, issue.6501, pp.111-114, 1994.
DOI : 10.1038/372111a0

M. J. Powell, Restart procedures for the conjugate gradient method, Mathematical Programming, vol.11, issue.1, pp.241-54, 1977.
DOI : 10.1007/BF01593790

A. C. Prats, C. Roy, P. A. Wang, M. Erard, V. Housset et al., cis elements and trans-acting factors involved in dimer formation of murine leukemia virus RNA, J Virol, vol.64, pp.774-83, 1990.

J. H. Prestegard, H. M. Hashimi, and J. R. Tolman, NMR structures of biomolecules using field oriented media and residual dipolar couplings, Quarterly Reviews of Biophysics, vol.33, issue.4, pp.371-424, 2000.
DOI : 10.1017/S0033583500003656

E. V. Puglisi and J. D. Puglisi, Nuclear magnetic resonance spectroscopy of RNA, RNA structure and function, pp.117-163, 1998.

R. Rahmouni, Z-DNA as a probe for localized supercoiling in vivo, Molecular Microbiology, vol.85, issue.2, pp.569-72, 1992.
DOI : 10.1016/0092-8674(88)90163-8

G. Ravishanker, S. Swaminathan, D. L. Beveridge, R. Lavery, and H. Sklenar, Conformational and Helicoidal Analysis of 30 PS of Molecular Dynamics on the d(CGCGAATTCGCG) Double Helix: ???Curves???, Dials and Windows, Journal of Biomolecular Structure and Dynamics, vol.11, issue.4, pp.669-99, 1989.
DOI : 10.1038/283743a0

URL : https://hal.archives-ouvertes.fr/hal-00313451

A. Rein, Retroviral RNA packaging: a review, Arch Virol, vol.9, pp.513-535, 1994.
DOI : 10.1007/978-3-7091-9326-6_49

A. Rich, Speculation on the Biological Roles of Left-Handed Z-DNA, Annals of the New York Academy of Sciences, vol.31, issue.1 DNA Damage, pp.1-17, 1995.
DOI : 10.1073/pnas.90.8.3339

A. Rich, A. Nordheim, and A. H. Wang, The Chemistry and Biology of Left-Handed Z-DNA, Annual Review of Biochemistry, vol.53, issue.1, pp.791-846, 1984.
DOI : 10.1146/annurev.bi.53.070184.004043

J. D. Robertus, J. E. Ladner, J. T. Finch, D. Rhodes, R. S. Brown et al., Structure of yeast phenylalanine tRNA at 3 ??? resolution, Nature, vol.1, issue.5467, pp.546-51, 1974.
DOI : 10.1038/250546a0

M. A. Rosen, L. Shapiro, and D. J. Patel, Solution structure of a trinucleotide A-T-A bulge loop within a DNA duplex, Biochemistry, vol.31, issue.16, pp.4015-4041, 1992.
DOI : 10.1021/bi00131a017

W. Saenger, Principles of nucleic acid structure, 1984.
DOI : 10.1007/978-1-4612-5190-3

K. Sakaguchi, N. Zambrano, E. T. Baldwin, B. A. Shapiro, J. W. Erickson et al., Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein., Proceedings of the National Academy of Sciences, vol.90, issue.11, pp.5219-5242, 1993.
DOI : 10.1073/pnas.90.11.5219

J. Santalucia, . Jr, R. Kierzek, and D. H. Turner, Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin, Science, vol.256, issue.5054, pp.217-226, 1992.
DOI : 10.1126/science.1373521

J. Santalucia, . Jr, and D. H. Turner, Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics, Biochemistry, vol.32, issue.47, pp.12612-12635, 1993.
DOI : 10.1021/bi00210a009

S. G. Schaaf, J. Beck, and M. Nassal, A Small 2'-OH- and Base-dependent Recognition Element Downstream of the Initiation Site in the RNA Encapsidation Signal Is Essential for Hepatitis B Virus Replication Initiation, Journal of Biological Chemistry, vol.274, issue.53, pp.37787-94, 1999.
DOI : 10.1074/jbc.274.53.37787

C. Scheurer, N. Skrynnikoc, S. F. Lienin, S. K. Straus, R. Brüschweiler et al., Effects of dynamics and environment of 15N chemical shielding anisotropy in proteins. A combination of density functional theory, molecular dynamics simulation, and NMR relaxation, J Am Chem Soc, vol.121, pp.4230-4231, 1999.

W. Shepard, W. B. Cruse, R. Fourme, E. De-la-fortelle, and T. Prangé, A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 ?? resolution, Structure, vol.6, issue.7, pp.849-61, 1998.
DOI : 10.1016/S0969-2126(98)00087-2

M. J. Sippl and H. A. Scheraga, Cayley-Menger coordinates., Proceedings of the National Academy of Sciences, vol.83, issue.8, pp.2283-2290, 1986.
DOI : 10.1073/pnas.83.8.2283

D. E. Smith, J. Y. Su, and F. M. Jucker, Efficient enzymatic synthesis of 13C,15N- labeled DNA for NMR studies, Journal of Biomolecular NMR, vol.10, issue.3, pp.245-53, 1997.
DOI : 10.1023/A:1018358602001

K. Snoussi, S. Nonin-lecomte, and J. L. Leroy, The RNA i-motif, Journal of Molecular Biology, vol.309, issue.1, pp.139-53, 2001.
DOI : 10.1006/jmbi.2001.4618

H. M. Sobell, Molecular Mechanism for Genetic Recombination, Proceedings of the National Academy of Sciences, vol.69, issue.9, pp.2483-2490, 1972.
DOI : 10.1073/pnas.69.9.2483

D. Söll, Transfert RNA: an RNA for all seasons in, The RNA World, pp.157-84, 1993.

E. G. Stein, L. M. Rice, and A. T. Brunger, Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation, Journal of Magnetic Resonance, vol.124, issue.1, pp.154-64, 1997.
DOI : 10.1006/jmre.1996.1027

N. Sugimoto, R. Kierzek, S. M. Freier, and D. H. Turner, Energetics of internal GU mismatches in ribooligonucleotide helixes, Biochemistry, vol.25, issue.19, pp.5755-5764, 1986.
DOI : 10.1021/bi00367a061

W. I. Sundquist and S. Heaphy, Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA [see comments], Proc Natl Acad Sci, pp.3393-3400, 1993.

A. A. Szewczak and P. B. Moore, The Sarcin/Ricin Loop, a Modular RNA, Journal of Molecular Biology, vol.247, issue.1, pp.81-98, 1995.
DOI : 10.1006/jmbi.1994.0124

K. Takahashi, S. Baba, Y. Hayashi, Y. Koyanagi, N. Yamamoto et al., NMR Analysis of Intra- and Inter-Molecular Stems in the Dimerization Initiation Site of the HIV-1 Genome, Journal of Biochemistry, vol.127, issue.4, pp.681-687, 2000.
DOI : 10.1093/oxfordjournals.jbchem.a022657

J. Tanikawa, Y. Nishimura, I. Hirao, and K. Miura, NMR spectroscopic study of single-stranded DNA fragments of d(CGGCGAAAGCCG) and d (CGGCGAAAAGCCG), Nucleic Acids Symp Ser, vol.25, pp.47-55, 1991.

V. Theilleux-delalande, Les interactions ARN/protéine de nucléocapside chez VIH-1 : leurs implications dans les relations structure-fonction in vitro, Thèse de doctorat, 1998.

C. Thibaudeau, J. Plavec, N. Garg, A. Pachikin, and J. Chattopadhyaya, How Does the Electronegativity of the Substituent Dictate the Strength of the Gauche Effect?, Journal of the American Chemical Society, vol.116, issue.9, pp.4038-4043, 1994.
DOI : 10.1021/ja00088a043

N. Tjandra and A. Bax, Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium [see comments] [published erratum appears in Science, Science, vol.278, issue.278, pp.1697-1111, 1997.

G. Varani, Exceptionally Stable Nucleic Acid Hairpins, Annual Review of Biophysics and Biomolecular Structure, vol.24, issue.1, pp.379-404, 1995.
DOI : 10.1146/annurev.bb.24.060195.002115

L. Verlet, Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules, Physical Review, vol.159, issue.1, pp.98-105, 1967.
DOI : 10.1103/PhysRev.159.98

J. D. Waston and F. H. Crick, The molecular structure of nucleic acids. A structure for deoxyribose nucleic acids, Nature, vol.171, pp.737-746, 1953.

K. B. Wiberg, Intramolecular interactions in molecular mechanics calculations, Computers & Chemistry, vol.1, issue.3, pp.221-224, 1977.
DOI : 10.1016/0097-8485(77)85013-4

S. S. Wijmenga, M. Kruithof, and C. W. Hilbers, Analysis of 1H chemical shifts in DNA : Assesment of the reliability of 1H chemical shift calculations for use in structure refinement, Journal of Biomolecular NMR, vol.10, issue.4, pp.337-50, 1997.
DOI : 10.1023/A:1018348123074

S. S. Wijmenga, M. M. Mooren, and C. W. Hilbers, NMR of macromolecules. A pratical approach, 1993.

S. S. Wijmenga and B. N. Van-buuren, The use of NMR methods for conformational studies of nucleic acids, Progress in Nuclear Magnetic Resonance Spectroscopy, vol.32, issue.4, pp.287-387, 1998.
DOI : 10.1016/S0079-6565(97)00023-X

P. J. Wilson, R. D. Amos, and N. C. Handy, Density functional predictions for magnetizabilities and nuclear shielding constants, Molecular Physics, vol.2, issue.6, pp.757-68, 1999.
DOI : 10.1016/S0009-2614(98)01201-9

W. D. Wilson and R. L. Jones, P NMR chemical shift and relaxation investigation, Nucleic Acids Research, vol.10, issue.4, pp.1399-410, 1982.
DOI : 10.1093/nar/10.4.1399

B. Wimberly, G. Varani, I. Tinoco, and . Jr, The conformation of loop E of eukaryotic 5S ribosomal RNA, Biochemistry, vol.32, issue.4, pp.1078-87, 1993.
DOI : 10.1021/bi00055a013

D. S. Wishart, B. D. Sykes, and F. M. Richards, The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy, Biochemistry, vol.31, issue.6, pp.1647-51, 1992.
DOI : 10.1021/bi00121a010

C. R. Woese, S. Winker, and R. R. Gutell, Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"., Proceedings of the National Academy of Sciences, vol.87, issue.21, pp.8467-71, 1990.
DOI : 10.1073/pnas.87.21.8467

S. I. Yamakage, T. V. Maltseva, F. P. Nilson, A. Foldesi, and J. Chattopadhyaya, Deuteriation of sugar protons simplify NMR assignments and structure determination of large oligonucleotide by the 1H-NMR window approach, Nucleic Acids Res, vol.21, pp.5005-5016, 1993.

X. L. Zhang and D. J. Patel, Solution structure of the luzopeptin-DNA complex, Biochemistry, vol.30, issue.16, pp.4026-4067, 1991.
DOI : 10.1021/bi00230a030

S. B. Zimmerman and B. H. Pheiffer, A direct demonstration that the ethanol-induced transition of DNA is between the A and B forms: an X-ray diffraction study, Journal of Molecular Biology, vol.135, issue.4, pp.1023-1030, 1979.
DOI : 10.1016/0022-2836(79)90526-6

G. R. Zimmermann, R. D. Jenison, C. L. Wick, J. P. Simorre, and A. Pardi, Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA, Nature Structural Biology, vol.253, issue.8, pp.644-653, 1997.
DOI : 10.1006/jmbi.1996.0690