T. Lindahl and D. Barnes, Repair of endogenous DNA damage, Cold Spring Harb Symp Quant Biol, vol.65, pp.127-133, 2000.

F. Bray, J. Ferlay, I. Soerjomataram, R. L. Siegel, L. A. Torre et al., Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA: a cancer journal for clinicians, vol.68, issue.6, pp.394-424, 2018.

J. H. Hoeijmakers, Genome maintenance mechanisms for preventing cancer, Nature, issue.6835, p.366, 2001.

J. D. Watson and F. H. Crick, A structure for deoxyribose nucleic acid, Nature, vol.171, pp.737-738, 1953.

:. User and . Sponk, Comparison of a single-stranded RNA and a double-stranded DNA with their corresponding nucleobases, 2010.

C. A. Davey, D. F. Sargent, K. Luger, A. W. Maeder, and T. J. Richmond, Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution, Journal of molecular biology, issue.5, pp.1097-1113, 2002.

T. Lindahl and D. Barnes, Repair of endogenous DNA damage, Cold Spring Harb Symp Quant Biol, vol.65, pp.127-133, 2000.

T. S. Dexheimer, DNA repair pathways and mechanisms, DNA repair of cancer stem cells, pp.19-32, 2013.

R. De-bont and N. Van-larebeke, Endogenous DNA damage in humans: a review of quantitative data, Mutagenesis, vol.19, issue.3, pp.169-185, 2014.

O. D. Schärer, Chemistry and biology of DNA repair, Angewandte Chemie International Edition, vol.42, issue.26, pp.2946-2974, 2003.

Y. Qi, M. C. Spong, K. Nam, A. Banerjee, S. Jiralerspong et al., Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme, Nature, vol.462, issue.7274, p.762, 2009.

S. Boiteux and M. Guillet, Abasic sites in DNA: repair and biological consequences in Saccharomyces cerevisiae, DNA repair, vol.3, issue.1, pp.1-12, 2004.

L. A. Loeb and B. D. Preston, Mutagenesis by apurinic/apyrimidinic sites. Annual review of genetics, vol.20, pp.201-230, 1986.

K. S. Gates, An overview of chemical processes that damage cellular DNA: spontaneous hydrolysis, alkylation, and reactions with radicals, Chemical research in toxicology, vol.22, issue.11, pp.1747-1760, 2009.

S. Barker, M. Weinfeld, J. Zheng, L. Li, and D. Murray, Identification of mammalian proteins cross-linked to DNA by ionizing radiation, Journal of Biological Chemistry, vol.280, issue.40, pp.33826-33838, 2005.

Y. W. Kow, Repair of deaminated bases in DNA, Free Radical Biology and Medicine, vol.33, issue.7, pp.886-893, 2002.

L. Miller-fleming, V. Olin-sandoval, K. Campbell, and M. Ralser, Remaining mysteries of molecular biology: the role of polyamines in the cell, Journal of molecular biology, vol.427, issue.21, pp.3389-3406, 2015.

A. E. Pegg, Functions of Polyamines in Mammals, Journal of Biological Chemistry, vol.291, pp.14904-14912, 2016.

A. J. Michael, Polyamines in eukaryotes, bacteria, and archaea, Journal of Biological Chemistry, issue.29, pp.14896-14903, 2018.

B. G. Feuerstein, L. D. Williams, H. S. Basu, and L. J. Marton, Implications and concepts of polyamine-nucleic acid interactions, Journal of Cellular Biochemistry, vol.46, pp.37-47, 1991.

N. Minois, D. Carmona-gutierrez, and F. Madeo, Polyamines in aging and disease, Aging (Albany NY), issue.3, p.716, 2011.

L. C. Gosule and J. A. Schellman, DNA condensation with polyamines: I. Spectroscopic studies, Journal of Molecular Biology, vol.121, pp.311-326, 1978.

N. Y. Tretyakova, A. Groehler, J. , and S. , DNA-Protein Cross-Links: Formation, Structural Identities, and Biological Outcomes, Accounts of Chemical Research, vol.48, pp.1631-1644, 2015.

J. Bai, Y. Zhang, Z. Xi, M. M. Greenberg, and C. Zhou, Oxidation of 8-Oxo-7,8-dihydro-2-deoxyguanosine Leads to Substantial DNA-Histone Cross-Links within Nucle-osome Core Particles, Chemical Research in Toxicology, vol.31, pp.1364-1372, 2018.

D. Esparza, J. Mincitar, N. Tran, A. Ramos, K. Miller et al., , 2016.

, Chemical and Biochemical Stability of Guanine Lysine Crosslinks Formed by Guanine Oxidation, The FASEB Journal, vol.30, issue.1_supplement, pp.1050-1052

R. E. Johnson, L. Haracska, S. Prakash, and L. Prakash, Role of DNA polymerase eta in the bypass of a (6-4) TT photoproduct, Mol. Cell. Biol, vol.21, pp.3558-63, 2001.

G. P. Pfeifer, Formation and Processing of UV Photoproducts: Effects of DNA Sequence and Chromatin Environment, Photochem. Photobiol, vol.65, pp.270-283, 1997.

S. Mouret, M. Charveron, A. Favier, J. Cadet, and T. Douki, Differential repair of UVB-induced cyclobutane pyrimidine dimers in cultured human skin cells and whole human skin, DNA Repair (Amst), vol.7, pp.704-712, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02054600

A. Ziegler, D. J. Leffell, S. Kunala, H. W. Sharma, M. Gailani et al., Mutation hotspots due to sunlight in the p53 gene of nonmelanoma skin cancers, Proc. Natl. Acad. Sci. U

S. A. , , vol.90, pp.4216-4236, 1993.

D. E. Brash, J. A. Rudolph, J. A. Simon, A. Lin, G. J. Mckenna et al., A role for sunlight in skin cancer: UV-induced p53 mutations in squamous cell carcinoma, Proc. Natl. Acad. Sci. U. S. A, vol.88, pp.10124-10132, 1991.

C. W. Lawrence, P. E. Gibbs, A. Borden, M. J. Horsfall, and B. J. Kilbey, Mutagenesis induced by single UV photoproducts in E. coli and yeast, Mutat. Res. Toxicol, vol.299, pp.157-163, 1993.

J. S. Taylor, Unraveling the Molecular Pathway from Sunlight to Skin Cancer, Acc. Chem. Res, vol.27, pp.76-82, 1994.

S. Her, D. A. Jaffray, and C. Allen, Gold nanoparticles for applications in cancer radiotherapy: Mechanisms and recent advancements, vol.109, pp.84-101, 2017.

M. Misawa and J. Takahashi, Generation of reactive oxygen species induced by gold nanoparticles under x-ray and UV Irradiations, Nanomedicine: Nanotechnology, Biology and Medicine, vol.7, issue.5, pp.604-614, 2011.

X. D. Zhang, Z. Luo, J. Chen, X. Shen, S. Song et al., Ultrasmall Au10?12 (SG)10?12 nanomolecules for high tumor specificity and cancer radiotherapy, Advanced materials, vol.26, issue.26, pp.4565-4568, 2014.

F. Baletto, Structural properties of sub nanometer metallic clusters, Journal of Physics: Condensed Matter, 2018.

X. D. Zhang, J. Chen, Z. Luo, D. Wu, X. Shen et al.,

S. Fan, F. Baletto, R. Ferrando, A. Fortunelli, F. Montalenti et al., Enhanced Tumor Accumulation of Sub-2 nm Gold Nanoclusters for Cancer Radiation Therapy, Advanced healthcare materials, vol.3, issue.1, pp.133-141, 2014.

, Crossover among structural motifs in transition and noble-metal clusters, J. Chem. Phys, vol.116, issue.9, pp.3856-3863, 2002.

F. Baletto and R. Ferrando, Structural properties of nanoclusters: Energetic, thermodynamic, and kinetic effects, Rev. Mod. Phys, vol.77, issue.1, p.371, 2005.

O. D. Häberlen, S. Chung, M. Stener, and N. Rösch, From clusters to bulk: a relativistic density functional investigation on a series of gold clusters Au n, n=6,?,147, J. Chem. Phys, vol.106, pp.5189-5201, 1997.

X. D. Zhang, D. Wu, X. Shen, J. Chen, Y. M. Sun et al.,

X. J. , Size-dependent radiosensitization of PEG-coated gold nanoparticles for cancer radiation therapy, Biomaterials, vol.33, issue.27, pp.6408-6419, 2012.

M. Gilles, E. Brun, and C. Sicard-roselli, Gold nanoparticles functionalization notably decreases radiosensitization through hydroxyl radical production under ionizing radiation, Colloids and Surfaces B: Biointerfaces, vol.123, pp.770-777, 2014.

F. Xiao, Y. Zheng, P. Cloutier, Y. He, D. Hunting et al., , 2011.

, On the role of low-energy electrons in the radiosensitization of DNA by gold nanoparticles, Nanotechnology, vol.22, issue.46, p.465101

X. Wang, X. Wang, X. Bai, L. Yan, T. Liu et al.,

, Nanoparticle Ligand Exchange and Its Effects at the Nanoparticle-Cell Membrane Interface, Nano letters, vol.19, issue.1, pp.8-18

W. N. Rahman, N. Bishara, T. Ackerly, C. F. He, P. Jackson et al., Enhancement of radiation effects by gold nanoparticles for superficial radiation therapy, Nanomedicine: Nanotechnology, Biology and Medicine, vol.5, issue.2, pp.136-142, 2009.

J. V. Jokerst, T. Lobovkina, R. N. Zare, and S. S. Gambhir, , 2011.

, Nanoparticle PEGylation for imaging and therapy, Nanomedicine, vol.6, issue.4, pp.715-728

J. S. Suk, Q. Xu, N. Kim, J. Hanes, and L. M. Ensign, PEGylation as a strategy for improving nanoparticle-based drug and gene delivery, Advanced drug delivery reviews, vol.99, pp.28-51, 2016.

A. Reznickova, P. Slepicka, N. Slavikova, M. Staszek, and V. Svorcik, Preparation, aging and temperature stability of, 2017.

M. Born, J. R. Oppenheimer, and A. , , vol.84, p.457, 1927.

D. R. Hartree, The wave mechanics of an atom with a non-Coulomb central field. Part I. Theory and methods, Mathematical Proceedings of the Cambridge Philosophical Society, vol.24, pp.89-110, 1928.

P. Hohenberg and W. Kohn, Inhomogeneous electron gas, Physical review, vol.136, issue.3B, p.864, 1964.

W. Kohn and L. J. Sham, Self-consistent equations including exchange and correlation effects, Physical review, issue.4A, p.1133, 1965.

D. M. Ceperley and B. J. Alder, Ground state of the electron gas by a stochastic method, Physical Review Letters, issue.7, p.566, 1980.

J. P. Perdew and W. Yue, Accurate and simple density functional for the electronic exchange energy: Generalized gradient approximation, Physical review B, issue.12, p.8800, 1986.

A. D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Physical review A, vol.38, issue.6, p.3098, 1998.

J. P. Perdew and Y. Wang, Accurate and simple analytic representation of the electron-gas correlation energy, Physical Review B, issue.23, p.13244, 1992.

J. P. Perdew, K. Burke, and M. Ernzerhof, Generalized gradient approximation made simple, Physical review letters, vol.77, issue.18, p.3865, 1996.

K. Burke, J. P. Perdew, and M. Ernzerhof, Generalized Gradient Approximation Made Simple, Phys. ReV. Lett, p.1396, 1996.

A. J. Logsdail, Z. Y. Li, and R. L. Johnston, Faceting preferences for AuN and PdN nanoclusters with high-symmetry motifs, Phys. Chem. Chem. Phys, vol.15, pp.8392-8400, 2013.

H. Li, L. Li, A. Pedersen, Y. Gao, N. Khetrapal et al., Magic-number gold nanoclusters with diameters from 1 to 3.5 nm: Relative stability and catalytic activity for CO oxidation, Nano Lett, vol.15, issue.1, pp.682-688, 2015.

F. Baletto, R. Ferrando, A. Fortunelli, F. Montalenti, and C. Mottet, Crossover among structural motifs in transition and noble-metal clusters, J. Chem. Phys, vol.116, issue.9, pp.3856-3863, 2002.

F. Baletto and R. Ferrando, Structural properties of nanoclusters: Energetic, thermodynamic, and kinetic effects, Rev. Mod. Phys, vol.77, issue.1, p.371, 2005.

J. M. Rahm and P. Erhart, Beyond Magic Numbers: Atomic Scale Equilibrium Nanoparticle Shapes for Any Size, Nano Lett, vol.17, issue.9, pp.5775-5781, 2017.

G. Kresse and J. Hafner, Ab initio Molecular Dynamics for Liquid Metals, Phys. Rev. B, p.47, 1993.

G. Kresse and J. Furthmüller, Efficiency of Ab-initio Total Energy Calculations for Metals and Semiconductors Using a Plane-wave Basis Set, Comput. Mat. Sci, vol.6, pp.15-50, 1996.

G. Kresse and J. Furthmüller, Efficient Iterative Schemes for Ab-initio Total-energy Calculations Using a Plane-wave Basis Set, Phys. Rev. B, p.11169, 1996.

J. P. Perdew, K. Burke, and M. Ernzerhof, Generalized Gradient Approximation Made Simple, Phys. Rev. Lett, vol.77, p.3865, 1996.

S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu, J. Chem. Phys, p.154104, 2010.

G. Kresse and D. Joubert, From Ultrasoft Pseudopotentials to the Projector Augmented-wave Method, Phys. Rev. B, p.1758, 1999.

B. K. Teo and N. J. Sloane, Magic numbers in polygonal and polyhedral clusters, Inorganic Chemistry, vol.24, issue.26, pp.4545-4558, 1985.

L. D. Marks, Modified Wulff constructions for twinned particles, Journal of Crystal Growth, issue.3, pp.556-566, 1983.

J. Uppenbrink and D. J. Wales, Structure and energetics of model metal clusters, The Journal of chemical physics, issue.11, pp.8520-8534, 1992.

R. Ferrando, J. Jellinek, and R. L. Johnston, Nanoalloys: from theory to applications of alloy clusters and nanoparticles, Chemical reviews, vol.108, issue.3, pp.845-910, 2008.

B. Wang, M. Liu, Y. Wang, and X. Chen, Structures and energetics of silver and gold nanoparticles, J. Phys. Chem. C, vol.115, issue.23, pp.11374-11381, 2011.

D. Gozzi, M. Tomellini, L. Lazzarini, and A. Latini, High-temperature determination of surface free energy of copper nanoparticles, The Journal of Physical Chemistry C, issue.28, pp.12117-12124, 2010.

K. K. Nanda, A. Maisels, F. E. Kruis, H. Fissan, and S. Stappert, Higher surface energy of free nanoparticles, Physical review letters, vol.91, issue.10, p.106102, 2003.

K. K. Nanda, A. Maisels, and F. E. Kruis, Surface tension and sintering of free gold nanoparticles, The Journal of Physical Chemistry C, vol.112, issue.35, pp.13488-13491, 2008.

F. Calle-vallejo, P. Sautet, and D. Loffreda, Understanding adsorption-induced effects on platinum nanoparticles: an energy-decomposition analysis. The journal of physical chemistry letters, vol.5, pp.3120-3124, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01116791

K. Kitaura and K. Morokuma, A New Energy Decomposition Scheme for Molecular Interactions within the Hartree-Fock Approximation, Int. J. Quantum Chem, vol.10, pp.325-340, 1976.

H. Umeyama and K. Morokuma, The Origin of Hydrogen Bonding. An Energy Decomposition Study, J. Am. Chem. Soc, vol.99, pp.1316-1332, 1977.

Y. Xue, Water monomer interaction with gold nanoclusters from van der Waals density functional theory, J. Chem. Phys, vol.2012, issue.2, p.24702

R. Nadler and J. F. Sanz, Effect of dispersion correction on the Au (1 1 1)-H2O interface: a first-principles study, J. Chem. Phys, vol.2012, issue.11, p.137

J. Carrasco, J. Klimes, and A. Michaelides, The role of van der Waals forces in water adsorption on metals, J. Chem. Phys, vol.138, 2013.

C. I. Chang, W. J. Lee, T. F. Young, S. P. Ju, C. W. Chang et al., Adsorption mechanism of water molecules surrounding Au nanoparticles of different sizes, J. Chem. Phys, vol.128, issue.15, p.154703, 2008.

R. F. De-morais, T. Kerber, F. Calle-vallejo, P. Sautet, and D. Loffreda, Capturing solvation effects at a liquid/nanoparticle interface by Ab Initio molecular dynamics: Pt201 immersed in water, Small, vol.2016, issue.38, pp.5312-5319
URL : https://hal.archives-ouvertes.fr/hal-01889540

M. Levitt, M. Hirschberg, R. Sharon, K. E. Laidig, and V. Daggett, Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution, J. Phys. Chem. B, vol.101, pp.5051-5061, 1997.

B. Santra, A. Michaelides, and M. Scheffler, Coupled cluster benchmarks of water monomers and dimers extracted from density-functional theory liquid water: the importance of monomer deformations, J. Chem. Phys, vol.131, issue.9, pp.124509-124510, 2009.

A. K. Soper, F. Bruni, and M. A. Ricci, Site-site pair correlation functions of water from 25 to 400 °C: Revised analysis of new and old diffraction data, J. Chem. Phys, vol.106, p.247, 1997.

E. Guardia, I. Skarmoutsos, and M. Masia, Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study, J. Phys. Chem. B, issue.29, pp.8926-8938, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01593537

S. Ju, A molecular dynamics simulation of the adsorption of water molecules surrounding an Au nanoparticle, J. Chem. Phys, vol.122, issue.6, pp.94718-94719, 2005.

Z. Y. Li, N. P. Young, M. Di-vece, S. Palomba, R. E. Palmer et al., Three-dimensional atomic-scale structure of size-selected gold nanoclusters, Nature, vol.451, pp.46-48, 2008.

D. M. Foster, R. Ferrando, and R. E. Palmer, Experimental determination of the energy difference between competing isomers of deposited, size-selected gold nanoclusters, Nature Communications, vol.9, p.1323, 2018.

S. R. Plant, L. Cao, and R. E. Palmer, Atomic Structure Control of Size-Selected Gold Nanoclusters during Formation, J. Am. Chem. Soc, vol.136, pp.7559-7562, 2014.

J. V. Jokerst, T. Lobovkina, R. N. Zare, and S. S. Gambhir, Nanoparticle PEGylation for imaging and therapy, Nanomedicine, vol.6, issue.4, pp.715-728, 2011.

X. Wang, X. Wang, X. Bai, L. Yan, T. Liu et al., Nanoparticle Ligand Exchange and Its Effects at the Nanoparticle-Cell Membrane Interface, Nano letters, vol.19, issue.1, pp.8-18, 2018.

E. Oh, J. B. Delehanty, K. E. Sapsford, K. Susumu, R. Goswami et al., Cellular uptake and fate of PEGylated gold nanoparticles is dependent on both cell-penetration peptides and particle size, ACS nano, vol.5, issue.8, pp.6434-6448, 2011.

O. D. Häberlen, S. Chung, M. Stener, and N. Rösch, From clusters to bulk: a relativistic density functional investigation on a series of gold clusters Au n, n = 6,···,147, J. Chem. Phys, vol.106, pp.5189-5201, 1997.

R. Ferrando, A. Fortunelli, and G. Rossi, Quantum effects on the structure of pure and binary metallic nanoclusters, Phys. Rev. B: Condens. Matter Mater. Phys, vol.72, p.85449, 2005.

H. Guesmi, N. B. Luque, E. Santos, and F. Tielens, Does the S? H Bond Always Break after Adsorption of an Alkylthiol on Au (111), Chemistry-A European Journal, vol.23, pp.1402-1408, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01397010

Y. Santiago-rodriguez, J. A. Herron, M. C. Curet-arana, and M. Mavrikakis, Atomic and molecular adsorption on Au (111), Surface Science, vol.627, pp.57-69, 2014.

C. M. Elvis, T. Ting, I. Popa, and . Paci, Surface-site reactivity in smallmolecule adsorption: A theoretical study of thiol binding on multi-coordinated gold clusters, Beilstein J. Nanotechnol, vol.7, pp.53-61, 2016.

C. Santosh-kumar-meena, D. Goldmann, M. Nassoko, T. Seydou, S. Marchandier et al., Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles, vol.11, pp.7371-7381, 2017.

D. N. Benoit, H. Zhu, M. H. Lilierose, R. A. Verm, N. Ali et al., Measuring the Grafting Density of Nanoparticles in Solution by Analytical Ultracentrifugation and Total Organic Carbon Analysis, Analytical Chemistry, vol.84, pp.9238-9245, 2012.

J. Lu, Y. Xue, R. Shi, J. Kang, C. Zhao et al., A non-sacrificial method for the quantification of poly(ethylene glycol) grafting density on gold nanoparticles for applications in nanomedicine, Chem. Sci, p.2067, 2019.

N. Ma, F. G. Wu, X. Zhang, Y. W. Jiang, H. R. Jia et al., Shape-dependent radiosensitization effect of gold nanostructures in cancer radiotherapy: comparison of gold nanoparticles, nanospikes, and nanorods, ACS applied materials & interfaces, vol.9, issue.15, pp.13037-13048, 2017.

J. L. Burta, J. L. Elechiguerraa, J. Reyes-gasga, J. Martin-montejano-carrizalesc, and M. Jose-yacaman, Beyond Archimedean solids: Star polyhedral gold nanocrystals, Journal of Crystal Growth, pp.285-681, 2005.

J. M. Cabrera-trujillo, *. , J. M. Montejano-carrizales, J. L. Rodr?´guez-ló-pez, W. Zhang et al., Nucleation and Growth of Stellated Gold Clusters: Experimental Synthesis and Theoretical Study, J. Phys. Chem. C, vol.114, pp.21051-21060, 2010.

A. Kabir and G. S. Kumar, Binding of the biogenic polyamines to deoxyribonucleic acids of varying base composition: base specificity and the associated energetics of the interaction, PLoS One, vol.8, issue.7, p.70510, 2013.

D. Case, , vol.12, 2012.

J. A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K. E. Hauser et al., ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB, Journal of chemical theory and computation, vol.11, issue.8, pp.3696-3713, 2015.

I. Ivani, P. D. Dans, A. Noy, A. Pérez, I. Faustino et al., & Portella, G. Parmbsc1: a refined force field for DNA simulations, Nature methods, vol.13, issue.1, p.55, 2016.

W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, Comparison of simple potential functions for simulating liquid water, The Journal of chemical physics, vol.79, issue.2, pp.926-935, 1983.

C. W. Hopkins, S. Le-grand, R. C. Walker, and A. E. Roitberg, Long-time-step molecular dynamics through hydrogen mass repartitioning, Journal of chemical theory and computation, vol.11, issue.4, pp.1864-1874, 2015.

S. Genheden and U. Ryde, The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities, Expert opinion on drug discovery, vol.10, issue.5, pp.449-461, 2015.

E. Bignon, C. H. Chan, C. Morell, A. Monari, J. L. Ravanat et al., Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity, Chemistry-A European Journal, vol.23, issue.52, pp.12845-12852, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01646327

A. Scrima, E. S. Fischer, S. Iwai, H. Gut, and N. H. Thoma, The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation, Cell, 1024.

T. Stoyanova, N. Roy, D. Kopanja, P. Raychaudhuri, and S. Bagchi, DDB2 (damaged-DNA binding protein 22) in nucleotide excision repair and DNA damage response, Cell Cycle, vol.8, pp.4067-71, 2009.

D. C. Bas, D. M. Rogers, and J. H. Jensen, Very fast prediction and rationalization of pKa values for protein-ligand complexes, Proteins Struct. Funct. Genet, vol.73, pp.765-783, 2008.

J. Wang, P. Cieplak, and P. A. Kollman, How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?, J. Comput. Chem, vol.21, pp.1049-1074, 2002.

J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al.,

, J. Comput. Chem, vol.26, pp.1781-1802, 2005.

R. Lavery, M. Moakher, J. H. Maddocks, D. Petkeviciute, and K. Zakrzewska, Conformational analysis of nucleic acids revisited: Curves+, Nucleic Acids Res, vol.37, pp.5917-5929, 2009.

A. Knips and M. Zacharias, Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage, Sci. Rep, 2017.

H. Fu, H. Zhang, H. Chen, X. Shao, C. Chipot et al., Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys, J. Phys. Chem. Lett, vol.9, pp.4738-4745, 2018.

S. Perrier, J. Hau, D. Gasparutto, J. Cadet, A. Favier et al., Characterization of Lysine-Guanine Cross-Links upon One-Electron Oxidation of a Guanine-Containing Oligonucleotide in the Presence of a Trilysine Peptide, Journal of the American Chemical Society, vol.128, pp.5703-5710, 2006.

H. Gattuso, X. Assfeld, and A. Monari, Modeling DNA electronic circular dichroism by QM/MM methods and Frenkel Hamiltonian, Theor. Chem. Acc, p.134, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02187406

C. I. Wang and J. S. Taylor, Site-specific effect of thymine dimer formation on dAn.dTn tract bending and its biological implications, Proc. Natl. Acad. Sci, vol.88, pp.9072-9076, 1991.

F. Dehez, H. Gattuso, E. Bignon, C. Morell, E. Dumont et al., Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates, Nucleic Acids Res, vol.45, pp.3654-3662, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01518937

M. G. Cooney and J. H. Miller, Calculated distortions of duplex DNA by a cis, syn cyclobutane thymine dimer are unaffected by a 3' TpA step, Nucleic Acids Res, vol.25, pp.1432-1436, 1997.

H. L. Lo, S. Nakajima, L. Ma, B. Walter, A. Yasui et al., Differential biologic effects of CPD and 6-4PP UV-induced DNA damage on the induction of apoptosis and cell-cycle arrest, BMC Cancer, issue.5, p.135, 2005.

J. Hu, O. Adebali, S. Adar, and A. Sancar, Dynamic maps of UV damage formation and repair for the human genome, Proc. Natl. Acad. Sci, 2007.

H. Gattuso, E. Durand, E. Bignon, C. Morell, A. G. Georgakilas et al., Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity, J. Phys. Chem. Lett, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01449702

C. H. Chan, F. Poignant, M. Beuve, E. Dumont, and D. Loffreda, A Water Solvation Shell can Transform Gold Metastable Nanoparticles in the Fluxional Regime, J. Phys. Chem. Lett, vol.10, issue.5, pp.1092-1098, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02057656

C. H. Chan, F. Poignant, M. Beuve, E. Dumont, and D. Loffreda, The PEGylation of

, Hydrated Gold Nanoparticles Promotes Stellated Clusters and Water Confinement inside the Organic Coating, 2019.

C. Hognon, C. H. Chan, C. Chipot, T. Douki, F. Dehez et al., Elucidating the different repair rates of cyclobutane pyrimidine dimers in DNA oligomers and their recognition by repair enzymes, 2019.

C. H. Chan, A. Monari, J. L. Ravanat, and E. Dumont, Guanine-lysine cross-linking: characterizing the association and chemical bond formation mechanisms from molecular dynamics, 2019.

M. Iachella, R. F. De-morais, C. H. Chan, and D. Loffreda, Introducing Composition-Stability Relations for Ordered Nanoalloys by Means of Surface Energy, 2019.

F. Poignant, H. Charfi, C. H. Chan, E. Dumont, D. Loffreda et al.,

M. Beuve, Monte Carlo study of the free radical production under keV photon irradiation in the presence of gold nanoparticles. PartI: macroscopic scale. 2019, to be submitted

. Docscilor,

, GdR NanOperando ( 28/11-30/11, 2018.

C. Forum,

. Or-nano, , vol.12, pp.6-14, 2017.

. Dna-damage and . Repair, Computations Meet Experiments

, Tutorials in Theoretical Chemistry

. Séjour-dans-le-laboratoire and . Srsmc, , vol.5, p.4

, Writing scientific articles more clearly in English, p.6

, Recherche et industrie : les enjeux de la Propriété Intellectuelle, p.12