R. M. Wartell and A. S. Benight, Thermal denaturation of DNA molecules: A comparison of theory with experiment, Physics Reports, vol.126, issue.2, pp.67-107, 1985.
DOI : 10.1016/0370-1573(85)90060-2

J. L. Leroy, M. Kochoyan, T. Huynh-dinh, and M. Guéron, Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton, Journal of Molecular Biology, vol.200, issue.2, pp.223-238, 1988.
DOI : 10.1016/0022-2836(88)90236-7

A. Montrichok, G. Gruner, and G. Zocchi, Trapping intermediates in the melting transition of DNA oligomers, Europhysics Letters (EPL), vol.62, issue.3, pp.452-458, 2003.
DOI : 10.1209/epl/i2003-00417-3

Y. Zeng, A. Montrichok, and G. Zocchi, Bubble Nucleation and Cooperativity in DNA Melting, Journal of Molecular Biology, vol.339, issue.1, pp.67-75, 2004.
DOI : 10.1016/j.jmb.2004.02.072

E. B. Brauns, C. J. Murphy, and M. A. Berg, Local Dynamics in DNA by Temperature-Dependent Stokes Shifts of an Intercalated Dye, Journal of the American Chemical Society, vol.120, issue.10, pp.2449-2456, 1998.
DOI : 10.1021/ja973207+

G. Altan-bonnet, A. Libchaber, and O. Krichevsky, Bubble Dynamics in Double-Stranded DNA, Physical Review Letters, vol.90, issue.13, pp.138101-138102, 2003.
DOI : 10.1103/PhysRevLett.90.138101

T. Douki, J. Ravanat, D. Angelov, J. R. Wagner, and J. Cadet, Effects of Duplex Stability on Charge-Transfer Efficiency within DNA, Top Curr. Chem, vol.236, pp.1-25, 2004.
DOI : 10.1007/b94409

D. Angelov, B. Beylot, and A. Spassky, Origin of the Heterogeneous Distribution of the Yield of Guanyl Radical in UV Laser Photolyzed DNA, Biophysical Journal, vol.88, issue.4, pp.2766-2778, 2005.
DOI : 10.1529/biophysj.104.049015

URL : https://hal.archives-ouvertes.fr/hal-00257508

S. C. Erfurth and W. L. Peticolas, Melting and premelting phenomenon in DNA by laser Raman scattering, Biopolymers, vol.8, issue.2, pp.247-264, 1975.
DOI : 10.1002/bip.1975.360140202

S. S. Chan, K. J. Breslauer, M. E. Hogan, D. J. Kessler, R. H. Austin et al., Physical studies of DNA premelting equilibria in duplexes with and without homo dA.cntdot.dT tracts: correlations with DNA bending, Biochemistry, vol.29, issue.26, pp.6161-6171, 1990.
DOI : 10.1021/bi00478a008

S. S. Chan, K. J. Breslauer, R. H. Austin, and H. M. , Thermodynamics and premelting conformational changes of phased (dA)5 tracts, Biochemistry, vol.32, issue.44, pp.11776-11784, 1993.
DOI : 10.1021/bi00095a005

L. Movileanu, J. M. Benevides, T. Jr, and G. J. , Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA, Nucleic Acids Research, vol.30, issue.17, pp.3767-3777, 2002.
DOI : 10.1093/nar/gkf471

B. H. Zimm, Theory of ``Melting'' of the Helical Form in Double Chains of the DNA Type, The Journal of Chemical Physics, vol.33, issue.5, pp.1349-1356, 1960.
DOI : 10.1063/1.1731411

Y. Kafri, D. Mukamel, and L. Peliti, Why is the DNA Denaturation Transition First Order?, Physical Review Letters, vol.85, issue.23, pp.4988-4991, 2000.
DOI : 10.1103/PhysRevLett.85.4988

M. Fixman and J. J. Freire, Theory of DNA melting curves, Biopolymers, vol.6, issue.12, pp.2693-2704, 1977.
DOI : 10.1002/bip.1977.360161209

E. Yeramian, Genes and the physics of the DNA double-helix, Gene, vol.255, issue.2, pp.139-150, 2000.
DOI : 10.1016/S0378-1119(00)00301-2

R. Blossey and E. Carlon, Reparametrizing the loop entropy weights: Effect on DNA melting curves, Physical Review E, vol.68, issue.6, p.61911, 2003.
DOI : 10.1103/PhysRevE.68.061911

R. A. Dimitrov, R. A. , M. Zuker, and M. , Prediction of Hybridization and Melting for Double-Stranded Nucleic Acids, Biophysical Journal, vol.87, issue.1, pp.215-226, 2004.
DOI : 10.1529/biophysj.103.020743

E. Carlon, A. Dkhissi, M. L. Malki, and R. Blossey, Stability domains of actin genes and genomic evolution, Physical Review E, vol.76, issue.5, p.51916, 2007.
DOI : 10.1103/PhysRevE.76.051916

M. Peyrard, Nonlinear dynamics and statistical physics of DNA, Nonlinearity, vol.17, issue.2, pp.1-40, 2004.
DOI : 10.1088/0951-7715/17/2/R01

M. Peyrard, Modelling DNA at the mesoscale: a challenge for nonlinear science?, Nonlinearity, vol.21, issue.6, pp.91-100, 2008.
DOI : 10.1088/0951-7715/21/6/T02

URL : https://hal.archives-ouvertes.fr/ensl-00309257

M. Peyrard and A. R. Bishop, Statistical mechanics of a nonlinear model for DNA denaturation, Physical Review Letters, vol.62, issue.23, pp.2755-2758, 1989.
DOI : 10.1103/PhysRevLett.62.2755

K. Drukker, G. Wu, and G. C. Schatz, Model simulations of DNA denaturation dynamics, The Journal of Chemical Physics, vol.114, issue.1, pp.579-590, 2001.
DOI : 10.1063/1.1329137

G. Weber, Sharp DNA denaturation due to solvent interaction, Europhysics Letters (EPL), vol.73, issue.5, pp.806-811, 2006.
DOI : 10.1209/epl/i2005-10466-6

N. Theodorakopoulos, T. Dauxois, M. Peyrard, and M. , Order of the Phase Transition in Models of DNA Thermal Denaturation, Physical Review Letters, vol.85, issue.1, pp.6-9, 2000.
DOI : 10.1103/PhysRevLett.85.6

T. Dauxois, M. Peyrard, M. Bishop, and A. R. , Entropy-driven DNA denaturation, Physical Review E, vol.47, issue.1, pp.44-47, 1993.
DOI : 10.1103/PhysRevE.47.R44

E. Giudice, P. Várnai, and R. Lavery, Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations, Nucleic Acids Research, vol.31, issue.5, pp.1434-1443, 2003.
DOI : 10.1093/nar/gkg239

URL : https://hal.archives-ouvertes.fr/hal-00313402

T. S. Van-erp, S. Cuesta-lópez, and M. Peyrard, Bubbles and denaturation in DNA, The European Physical Journal E, vol.28, issue.4, pp.421-434, 2006.
DOI : 10.1140/epje/i2006-10032-2

A. Campa and A. Giansanti, Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains, Physical Review E, vol.58, issue.3, pp.3585-3588, 1998.
DOI : 10.1103/PhysRevE.58.3585

O. Gotoh and Y. Tagashira, Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles, Biopolymers, vol.277, issue.5, pp.1033-1042, 1981.
DOI : 10.1002/bip.1981.360200513

W. Saenger, Principles of Nucleic Acid Structure, 1984.
DOI : 10.1007/978-1-4612-5190-3

J. Errami, M. Peyrard, and N. Theodorakopoulos, Modeling DNA beacons at the mesoscopic scale, The European Physical Journal E, vol.88, issue.4, pp.397-411, 2007.
DOI : 10.1140/epje/i2007-10200-x

URL : https://hal.archives-ouvertes.fr/ensl-00517615

T. Dauxois, M. Peyrard, M. Bishop, and A. R. , Dynamics and thermodynamics of a nonlinear model for DNA denaturation, Physical Review E, vol.47, issue.1, pp.684-695, 1993.
DOI : 10.1103/PhysRevE.47.684