F. Beaurain, D. Primo, C. Toulmé, J. Laguerre, and M. , Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer, Nucleic Acids Research, vol.31, issue.14, pp.4275-84, 2003.
DOI : 10.1093/nar/gkg467

N. Bendridi, M. Possedko, C. Chevalier, A. Helfer, Y. Benito et al., Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism, Genes Dev, vol.21, pp.1353-66, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00167517

C. Boiziau, E. Dausse, L. Yurchenko, and 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

K. Chang, I. Tinoco, and J. , 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. Chang, I. Tinoco, and J. , 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

D. Christ and G. Winter, Identification of functional similarities between proteins using directed evolution, Proceedings of the National Academy of Sciences, vol.100, issue.23, pp.13202-13208, 2003.
DOI : 10.1073/pnas.2134365100

L. Comolli, J. Pelton, I. Tinoco, and J. , Mapping of a protein-RNA kissing hairpin interface: Rom and Tar-Tar, Nucleic Acids Research, vol.26, issue.20, pp.4688-95, 1998.
DOI : 10.1093/nar/26.20.4688

F. Darfeuille, C. Cazenave, S. Gryaznov, F. Ducongé, D. Primo et al., -ACTIVATION RESPONSIVE (TAR) RNA OF THE HUMAN IMMUNODEFICIENCY VIRUS-1, Nucleosides, Nucleotides and Nucleic Acids, vol.26, issue.4-7, pp.441-450, 2001.
DOI : 10.1081/NCN-100002318

URL : https://hal.archives-ouvertes.fr/hal-01265411

D. Primo, C. Lebars, and I. , Determination of refractive index increment ratios for protein???nucleic acid complexes by surface plasmon resonance, Analytical Biochemistry, vol.368, issue.2, pp.148-55, 2007.
DOI : 10.1016/j.ab.2007.06.016

URL : https://hal.archives-ouvertes.fr/inserm-00173539

F. Ducongé, D. Primo, C. Toulmé, and J. , Is a Closing "GA Pair" a Rule for Stable Loop-Loop RNA Complexes?, Journal of Biological Chemistry, vol.275, issue.28, pp.21287-94, 2000.
DOI : 10.1074/jbc.M002694200

F. Ducongé and J. Toulmé, In vitro selection identifies key determinants for loop???loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1, RNA, vol.5, issue.12, pp.1605-1619, 1999.
DOI : 10.1017/S1355838299991318

W. Eberle, A. Pastore, C. Sander, and P. Rosch, The structure of ColE1 rop in solution, Journal of Biomolecular NMR, vol.169, issue.1, pp.71-82, 1991.
DOI : 10.1007/BF01874570

Y. Eguchi and J. Tomizawa, Complex formed by complementary RNA stem-loops and its stabilization by a protein: Function of ColE1 Rom protein, Cell, vol.60, issue.2, pp.199-209, 1990.
DOI : 10.1016/0092-8674(90)90736-X

Y. Eguchi and J. Tomizawa, Complexes formed by complementary RNA stem-loops, Journal of Molecular Biology, vol.220, issue.4, pp.831-873, 1991.
DOI : 10.1016/0022-2836(91)90356-B

E. Ennifar, P. Walter, B. Ehresmann, C. Ehresmann, and P. Dumas, Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site, Nature Structural Biology, vol.8, issue.12, pp.1064-1072, 2001.
DOI : 10.1038/nsb727

R. Fisher, M. Fivash, A. Stephen, N. Hagan, S. Shenoy et al., Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides, Nucleic Acids Research, vol.34, issue.2, pp.472-84, 1998.
DOI : 10.1093/nar/gkj442

R. Gregorian, J. Crothers, and D. , Determinants of RNA Hairpin Loop-Loop Complex Stability, Journal of Molecular Biology, vol.248, issue.5, pp.968-84, 1995.
DOI : 10.1006/jmbi.1995.0275

S. Jang, M. Jeong, R. Carter, E. Holbrook, L. Comolli et al., Novel crystal form of the ColE1 Rom protein, Acta Crystallographica Section D Biological Crystallography, vol.62, issue.6, pp.619-646, 2006.
DOI : 10.1107/S0907444906012388

L. Joss, T. Morton, M. Doyle, and D. Myszka, Interpreting Kinetic Rate Constants from Optical Biosensor Data Recorded on a Decaying Surface, Analytical Biochemistry, vol.261, issue.2, pp.203-213, 1998.
DOI : 10.1006/abio.1998.2744

C. Kim, I. Tinoco, and J. , A retroviral RNA kissing complex containing only two G{middle dot}C base pairs, Proceedings of the National Academy of Sciences, vol.97, issue.17, pp.9396-401, 2000.
DOI : 10.1073/pnas.170283697

M. Law, A. Rice, P. Lin, and I. Laird-offringa, The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA, RNA, vol.12, issue.7, pp.1168-78, 2006.
DOI : 10.1261/rna.75206

A. Lee and D. 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

P. Li, C. Bustamante, I. Tinoco, and J. , Unusual mechanical stability of a minimal RNA kissing complex, Proceedings of the National Academy of Sciences, vol.103, issue.43, 2006.
DOI : 10.1073/pnas.0607202103

T. Morton and D. Myszka, [13] Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors, Methods Enzymol, vol.295, pp.268-94, 1998.
DOI : 10.1016/S0076-6879(98)95044-3

D. Myszka, Improving biosensor analysis, Journal of Molecular Recognition, vol.273, issue.5, pp.279-84, 1999.
DOI : 10.1002/(SICI)1099-1352(199909/10)12:5<279::AID-JMR473>3.0.CO;2-3

J. Paillart, E. Skripkin, B. Ehresmann, C. Ehresmann, and R. Marquet, A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA., Proceedings of the National Academy of Sciences, vol.93, issue.11, pp.5572-5577, 1996.
DOI : 10.1073/pnas.93.11.5572

R. Marquet, Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA, J Mol Biol, vol.270, pp.36-49, 1997.

P. Predki, L. Nayak, M. Gottlieb, and L. Regan, Dissecting RNA-protein interactions: RNA-RNA recognition by Rop Survey of the year 2005 commercial optical biosensor literature, Cell Rich RL, Myszka DG. J Mol Recognit, vol.80, issue.19, pp.41-50, 1995.

M. Rist and J. Marino, Association of an RNA kissing complex analyzed using 2-aminopurine fluorescence, Nucleic Acids Research, vol.29, issue.11, pp.2401-2409, 2001.
DOI : 10.1093/nar/29.11.2401

S. Sjölander and C. Urbaniczky, Integrated fluid handling system for biomolecular interaction analysis, Analytical Chemistry, vol.63, issue.20, pp.2338-2383, 1991.
DOI : 10.1021/ac00020a025

Y. Song, P. Friebe, E. Tzima, C. Junemann, R. Bartenschlager et al., The Hepatitis C Virus RNA 3'-Untranslated Region Strongly Enhances Translation Directed by the Internal Ribosome Entry Site, Journal of Virology, vol.80, issue.23, pp.11579-88, 2006.
DOI : 10.1128/JVI.00675-06

T. Tumolo, L. Angnes, and M. Baptista, Determination of the refractive index increment (dn/dc) of molecule and macromolecule solutions by surface plasmon resonance Analysing structurefunction relationships with biosensors, Anal Biochem Cell Mol Life Sci, vol.333, issue.58, pp.273-279, 2001.