R. Klose, A. Bird, and P. Schorderet, Genomic DNA methylation: the mark and its mediators, Trends in Biochemical Sciences, vol.31, issue.2, pp.89-97, 2006.
DOI : 10.1016/j.tibs.2005.12.008

B. E. Bernstein, R. Jaenisch, E. S. Lander, A. Meissner, M. F. Denissenko et al., Dissecting Direct Reprogramming through Integrative Genomic Analysis Cytosine Methylation Determines Hot Spots of DNA Damage in the Human P53 Gene Sunlight Induces Pyrimidine Dimers Preferentially at 5-Methylcytosine Bases, Proc. Natl. Acad. Sci. USA 1997, pp.49-50, 1997.

L. Esposito, A. Banyasz, T. Douki, M. Perron, D. Markovitsi et al., Effect of C5-Methylation of Cytosine on the Photoreactivity of DNA: A Joint Experimental and Computational Study of TCG Trinucleotides, Journal of the American Chemical Society, vol.136, issue.31, pp.7-13, 2009.
DOI : 10.1021/ja5040478
URL : https://hal.archives-ouvertes.fr/hal-01075288

Y. H. You, C. Li, and G. P. Pfeifer, Involvement of 5-methylcytosine in sunlight-induced mutagenesis, Journal of Molecular Biology, vol.293, issue.3, pp.493-503, 1999.
DOI : 10.1006/jmbi.1999.3174

B. Vu, V. Cannistraro, L. Sun, and J. Taylor, DNA Synthesis Past a 5-Methylc-Containing Cis-Syn-Cyclobutane Pyrimidine Dimer by Yeast Pol Eta Is Highly Nonmutagenic Biochem, pp.9327-9335, 2006.

D. Markovitsi, T. Gustavsson, and I. Vayá, Fluorescence of DNA Duplexes: From Model Helices to Natural DNA, The Journal of Physical Chemistry Letters, vol.1, issue.22, pp.3271-3276, 2010.
DOI : 10.1021/jz101122t
URL : https://hal.archives-ouvertes.fr/hal-00538375

M. Mccullagh, F. Lewis, D. Markovitsi, T. Douki, and G. C. Schatz, Conformational Control of TT Dimerization in DNA Conjugates. A Molecular Dynamics Study, The Journal of Physical Chemistry B, vol.114, issue.15, pp.5215-5221, 2010.
DOI : 10.1021/jp100983t
URL : https://hal.archives-ouvertes.fr/hal-00480209

W. Lee and S. Matsika, QM/MM studies reveal pathways leading to the quenching of the formation of thymine dimer photoproduct by flanking bases, Phys. Chem. Chem. Phys., vol.129, issue.15, pp.9927-9935, 2015.
DOI : 10.1039/C5CP00292C

D. Onidas, D. Markovitsi, S. Marguet, A. Sharonov, and T. Gustavsson, Fluorescence Properties of DNA Nucleosides and Nucleotides:?? A Refined Steady-State and Femtosecond Investigation, The Journal of Physical Chemistry B, vol.106, issue.43, pp.11367-11374, 2002.
DOI : 10.1021/jp026063g
URL : https://hal.archives-ouvertes.fr/hal-00144518

/. Uvb and . Uvc, Processes in Model DNA Helices Studied by Time-Resolved Spectroscopy: Pitfalls and Tricks, J. Photochem. Photobiol. A-Chem, vol.183, pp.1-8, 2006.

S. Dixit, B. Jayaram, F. Lankas, and C. Laughton, A Systematic Molecular Dynamics Study of Nearest-Neighbor Effects on Base Pair and Base Pair Step Conformations and Fluctuations in B-DNA, Nucl. Ac. Res, vol.38, pp.299-313, 2010.

D. Ferguson, G. Seibel, and P. Kollman, Amber, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules

A. Perez, I. Marchan, D. Svozil, J. Sponer, T. E. Cheatham et al., Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of ??/?? Conformers, Biophysical Journal, vol.92, issue.11, pp.3817-3829, 2007.
DOI : 10.1529/biophysj.106.097782

T. E. Cheatham, P. Cieplak, and P. A. Kollman, Force Field with Improved Sugar Pucker Phases and Helical Repeat, Journal of Biomolecular Structure and Dynamics, vol.16, issue.4, pp.845-862, 1999.
DOI : 10.1021/jp953080f

D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo et al., The Amber biomolecular simulation programs, Journal of Computational Chemistry, vol.124, issue.16
DOI : 10.1002/jcc.20290

H. J. Berendsen, J. R. Grigera, and T. P. Straatsma, The missing term in effective pair potentials, The Journal of Physical Chemistry, vol.91, issue.24, pp.6269-6271, 1987.
DOI : 10.1021/j100308a038

F. Lankas, T. E. Cheatham, N. Spackova, P. Hobza, J. Langowski et al., Critical Effect of the N2 Amino Group on Structure, Dynamics, and Elasticity of DNA Polypurine Tracts, Biophysical Journal, vol.82, issue.5, pp.2592-2609, 2002.
DOI : 10.1016/S0006-3495(02)75601-4

W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1
DOI : 10.1016/0263-7855(96)00018-5

X. Lu and W. K. Olson, 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures, Nature Protocols, vol.7, issue.7, pp.1213-1227, 2008.
DOI : 10.1038/nprot.2008.104

D. Markovitsi, Electronic Excited States Responsible for Dimer Formation Upon Uv Absorption Directly by Thymine Strands: Joint Experimental and Theoretical Study, J. Am. Chem. Soc, vol.134, pp.14834-14845, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00732999

A. Sharonov, T. Gustavsson, S. Marguet, and D. Markovitsi, Photophysical properties of 5-methylcytidine, Photochemical & Photobiological Sciences, vol.2, issue.4, pp.362-364, 2003.
DOI : 10.1039/b212664h

J. M. Martínez, S. K. Elmroth, and L. Kloo, Influence of Sodium Ions on the Dynamics and Structure of Single-Stranded DNA Oligomers:?? A Molecular Dynamics Study, Journal of the American Chemical Society, vol.123, issue.49
DOI : 10.1021/ja0108786

A. Perez, C. Lara-castellazzi, F. Battistini, K. Collinet, O. Flores et al., Impact of Methylation on the Physical Properties of DNA, Biophysical Journal, vol.102, issue.9, pp.2140-2148, 2012.
DOI : 10.1016/j.bpj.2012.03.056

C. Bianchi and R. Zangi, Base-Flipping Propensities of Unmethylated, Hemimethylated, and Fully Methylated CpG Sites, The Journal of Physical Chemistry B, vol.117, issue.8, pp.2348-2358, 2013.
DOI : 10.1021/jp312145b

T. T. Ngo, J. Yoo, Q. Dai, Q. Zhang, C. He et al., Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability, Nature Communications, vol.4
DOI : 10.1038/ncomms10813

T. I. Yusufaly, Y. Li, and W. K. Olson, 5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics, The Journal of Physical Chemistry B, vol.117, issue.51
DOI : 10.1021/jp409887t

D. Markovitsi, UV-induced DNA Damage: The Role of Electronic Excited States, Photochemistry and Photobiology, vol.133, issue.1
DOI : 10.1111/php.12533
URL : https://hal.archives-ouvertes.fr/hal-01266776

I. Vayá, T. Gustavsson, T. Douki, Y. Berlin, and D. Markovitsi, Electronic Excitation Energy Transfer between Nucleobases of Natural DNA, J. Am. Chem. Soc, vol.134, pp.2012-11366

J. Chen, Y. Zhang, and B. Kohler, Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy, Top. Curr. Chem, vol.356, pp.39-87, 2015.
DOI : 10.1007/128_2014_570

F. Plasser, A. Aquino, H. Lischka, and D. Nachtigallová, Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach, Top. Curr. Chem, vol.356, pp.1-38, 2015.
DOI : 10.1007/128_2013_517

P. Changenet-barret, T. Gustavsson, D. Markovitsi, and I. Manet, Ultrafast Electron Transfer in Complexes of Doxorubicin with Human Telomeric G-Quadruplexes and GC Duplexes Probed by Femtosecond Fluorescence Spectroscopy, ChemPhysChem, vol.13, issue.9, pp.1-10, 2016.
DOI : 10.1002/cphc.201501091
URL : https://hal.archives-ouvertes.fr/cea-01426214

R. Improta, Photophysics and Photochemistry of Thymine Deoxy-Dinucleotide in Water: A PCM/TD-DFT Quantum Mechanical Study, The Journal of Physical Chemistry B, vol.116, issue.49, pp.14261-14274, 2012.
DOI : 10.1021/jp3093385

T. Douki and J. Cadet, Formation of Cyclobutane dimers and (6-4) Photoproducts upon Far-UV Photolysis of 5-Methylcytosine-Containing Dinucleoside Monophosphates, Biochemistry, vol.33, issue.39, pp.11942-11950, 1994.
DOI : 10.1021/bi00205a033

Z. Pan, M. Hariharan, J. D. Arkin, A. S. Jalilov, M. Mccullagh et al., Electron Donor-Acceptor Interactions with Flanking Purines Influence the Efficiency of, Thymine Photodimerization J. Am. Chem. Soc, vol.133134, pp.3611-3611, 2011.

K. Zakrzewska, Influence of Conformational Dynamics on the Exciton States of DNA Oligomers, J. Phys. Chem. B, vol.107, pp.13512-13522, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00094533

C. Ecoffet, D. Markovitsi, P. Millie, and J. Lemaistre, Electronic excitations in organized molecular systems. A model for columnar aggregates of ionic compounds, Chemical Physics, vol.177, issue.3, pp.629-643, 1993.
DOI : 10.1016/0301-0104(93)85028-7

D. Markovitsi, T. Gustavsson, and F. Talbot, Excited states and energy transfer among DNA bases in double helices, Photochemical & Photobiological Sciences, vol.5, issue.1?12, pp.717-724, 2007.
DOI : 10.1039/b705674e
URL : https://hal.archives-ouvertes.fr/hal-00162437

E. Emanuele, D. Markovitsi, P. Millié, and K. Zakrzewska, UV Spectra and Excitation Delocalization in DNA: Influence of the Spectral Width, ChemPhysChem, vol.348, issue.7, pp.1387-1392, 2005.
DOI : 10.1002/cphc.200500014
URL : https://hal.archives-ouvertes.fr/hal-00314943

T. Douki, J. A. Meador, I. Berard, and A. Wack, N4-Methylation of Cytosine Drastically Favors the Formation of (6-4) Photoproducts in a TCG Context, Photochemistry and Photobiology, vol.12, issue.1, pp.102-108, 2015.
DOI : 10.1111/php.12365

P. Clivio, J. Fourrey, and J. Gasche, DNA photodamage mechanistic studies: characterization of a thietane intermediate in a model reaction relevant to "6-4 lesions", Journal of the American Chemical Society, vol.113, issue.14
DOI : 10.1021/ja00014a065

S. Marguet and D. Markovitsi, Time-Resolved Study of Thymine Dimer Formation, Journal of the American Chemical Society, vol.127, issue.16
DOI : 10.1021/ja050648h
URL : https://hal.archives-ouvertes.fr/hal-00083445