M. L. Holmes-son, R. S. Appa, and S. A. Chow, 2 Molecular genetics and target site specificity of retroviral integration, Adv. Genet, vol.43, pp.33-69, 2001.
DOI : 10.1016/S0065-2660(01)43003-3

D. Suck, DNA recognition by structure-selective nucleases, Biopolymers, vol.92, issue.4, pp.405-421, 1997.
DOI : 10.1016/0167-4838(93)90227-I

M. E. Churchill, D. N. Jones, T. Glaser, H. Hefner, M. A. Searles et al., HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG, EMBO J, vol.14, pp.1264-1275, 1995.

J. Widom, Role of DNA sequence in nucleosome stability and dynamics, Quarterly Reviews of Biophysics, vol.34, issue.03, pp.269-324, 2001.
DOI : 10.1017/S0033583501003699

A. Lahm and D. Suck, DNase I-induced DNA conformation, Journal of Molecular Biology, vol.222, issue.3, pp.645-667, 1991.
DOI : 10.1016/0022-2836(91)90502-W

M. Laskowski, Deoxyribonuclease I, The Enzymes, 1971.

S. Moore, Pancreatic DNase, The Enzymes, 1981.
DOI : 10.1016/s1874-6047(08)60341-8

M. Brenowitz, D. F. Senear, M. A. Shea, and G. K. Ackers, [9] Quantitative DNase footprint titration: A method for studying protein-DNA interactions, Methods Enzymol, vol.130, pp.132-181, 1986.
DOI : 10.1016/0076-6879(86)30011-9

D. J. Galas and A. Schmitz, DNAase footprinting a simple method for the detection of protein-DNA binding specificity, Nucleic Acids Research, vol.5, issue.9, pp.3157-3170, 1978.
DOI : 10.1093/nar/5.9.3157

M. J. Lane, J. C. Dabrowiak, and J. N. Vournakis, Sequence specificity of actinomycin D and Netropsin binding to pBR322 DNA analyzed by protection from DNase I., Proc. Natl Acad. Sci. USA, pp.3260-3264, 1983.
DOI : 10.1073/pnas.80.11.3260

B. Sollner-webb, W. Melchior, &. Jr, and G. Felsenfeld, DNAase I, DNAase II and staphylococcal nuclease cut at different, yet symmetrically located, sites in the nucleosome core, Cell, vol.14, issue.3, pp.611-627, 1978.
DOI : 10.1016/0092-8674(78)90246-5

A. P. Boyle, S. Davis, H. P. Shulha, P. Meltzer, E. H. Margulies et al., High-Resolution Mapping and??Characterization of Open Chromatin across the Genome, Cell, vol.132, issue.2, pp.311-322, 2008.
DOI : 10.1016/j.cell.2007.12.014

J. R. Hesselberth, X. Chen, Z. Zhang, P. J. Sabo, R. Sandstrom et al., Global mapping of protein-DNA interactions in vivo by digital genomic footprinting, Nature Methods, vol.8, issue.4, pp.283-289, 2009.
DOI : 10.1073/pnas.0601091103

A. Kim, S. H. Song, M. Brand, and A. Dean, Nucleosome and transcription activator antagonism at human ??-globin locus control region DNase I hypersensitive sites, Nucleic Acids Research, vol.35, issue.17, pp.5831-5838, 2007.
DOI : 10.1093/nar/gkm620
URL : http://doi.org/10.1093/nar/gkm620

A. Y. Lee and C. M. Chiang, Chromatin Adaptor Brd4 Modulates E2 Transcription Activity and Protein Stability, Journal of Biological Chemistry, vol.70, issue.5, pp.2778-2786, 2009.
DOI : 10.1074/jbc.M314340200
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631962

A. Radwan, A. Younis, P. Luykx, and S. Khuri, Prediction and analysis of nucleosome exclusion regions in the human genome, BMC Genomics, vol.9, issue.1, p.186, 2008.
DOI : 10.1186/1471-2164-9-186

D. Z. Staynov, DNase I footprinting of the nucleosome in whole nuclei, Biochemical and Biophysical Research Communications, vol.372, issue.1, pp.226-229, 2008.
DOI : 10.1016/j.bbrc.2008.05.024

Y. Zhang, H. Shin, J. S. Song, Y. Lei, and X. S. Liu, Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq, BMC Genomics, vol.9, issue.1, p.537, 2008.
DOI : 10.1186/1471-2164-9-537

H. R. Drew, Structural specificities of five commonly used DNA nucleases, Journal of Molecular Biology, vol.176, issue.4, pp.535-557, 1984.
DOI : 10.1016/0022-2836(84)90176-1

H. R. Drew and A. A. Travers, DNA structural variations in the E. coli tyrT promoter, Cell, vol.37, issue.2, pp.491-502, 1984.
DOI : 10.1016/0092-8674(84)90379-9

H. R. Drew and A. A. Travers, Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities, Nucleic Acids Research, vol.13, issue.12, pp.4445-4467, 1985.
DOI : 10.1093/nar/13.12.4445

S. A. Weston, A. Lahm, and D. Suck, X-ray structure of the DNase I-d(GGTATACC)2 complex at 2??3?? resolution, Journal of Molecular Biology, vol.226, issue.4, pp.1237-1256, 1992.
DOI : 10.1016/0022-2836(92)91064-V

S. Weston and D. Suck, X-ray structures of two single-residue mutants of DNase I: H134Q and Y76A, "Protein Engineering, Design and Selection", vol.6, issue.4, pp.349-357, 1993.
DOI : 10.1093/protein/6.4.349

A. J. Doherty, A. F. Worrall, and B. A. Connolly, The Roles of Arginine 41 and Tyrosine 76 in the coupling of DNA Recognition to Phosphodiester Bond Cleavage by DNase I: a Study using Site-directed Mutagenesis, Journal of Molecular Biology, vol.251, issue.3, pp.366-377, 1995.
DOI : 10.1006/jmbi.1995.0440

M. A. Warren, S. J. Evans, and B. A. Connolly, Effects of non-conservative changes to tyrosine 76, a key DNA binding residue of DNase I, on phosphodiester bond cleavage and DNA hydrolysis selectivity, Protein Engineering Design and Selection, vol.10, issue.3, pp.279-283, 1997.
DOI : 10.1093/protein/10.3.279

D. Suck, DNA recognition by DNase I, Journal of Molecular Recognition, vol.85, issue.2, pp.65-70, 1994.
DOI : 10.1007/978-3-642-84292-4_11

G. P. Lomonossoff, P. J. Butler, and A. Klug, Sequence-dependent variation in the conformation of DNA, Journal of Molecular Biology, vol.149, issue.4, pp.745-760, 1981.
DOI : 10.1016/0022-2836(81)90356-9

R. Nussinov, B. Shapiro, L. E. Lipkin, J. V. Maizel, and . Jr, DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation, Journal of Molecular Biology, vol.177, issue.4, pp.591-607, 1984.
DOI : 10.1016/0022-2836(84)90039-1

R. E. Dickerson and H. R. Drew, Structure of a B-DNA dodecamer, Journal of Molecular Biology, vol.149, issue.4, pp.761-786, 1981.
DOI : 10.1016/0022-2836(81)90357-0

I. Brukner, R. Sanchez, D. Suck, and S. Pongor, Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides, EMBO J, vol.14, pp.1812-1818, 1995.

R. E. Dickerson, DNA bending: the prevalence of kinkiness and the virtues of normality, Nucleic Acids Research, vol.26, issue.8, pp.1906-1926, 1998.
DOI : 10.1093/nar/26.8.1906

B. Hartmann and R. Lavery, DNA structural forms, Quarterly Reviews of Biophysics, vol.14, issue.04, pp.309-368, 1996.
DOI : 10.1002/bip.360280608
URL : https://hal.archives-ouvertes.fr/hal-00312970

C. Yoon, G. G. Prive, D. S. Goodsell, and R. E. Dickerson, Structure of an alternating-B DNA helix and its relationship to A-tract DNA., Proc. Natl Acad. Sci. USA, pp.6332-6336, 1988.
DOI : 10.1073/pnas.85.17.6332

J. E. Herrera and J. B. Chaires, Characterization of Preferred Deoxyribonuclease I Cleavage Sites, Journal of Molecular Biology, vol.236, issue.2, pp.405-411, 1994.
DOI : 10.1006/jmbi.1994.1152

K. R. Fox, . Cgcgaattcgcg, C. Cgcgttaacgcg, C. , C. et al., Probing the conformations of eight cloned-DNA dodecamers; CGCGAATTCGCG, CGCGTTAACGCG, CGCGTATACGCG, CGCGATATCGCG, CGCAAATTTGCG, CGCTTTAAAGCG, CGCGGATCCGCG and CGCGGTACCGCG, Nucleic Acids Research, vol.20, issue.24, pp.6487-6493, 1992.
DOI : 10.1093/nar/20.24.6487

M. E. Hogan, M. W. Roberson, and R. H. Austin, DNA flexibility variation may dominate DNase I cleavage., Proc. Natl Acad. Sci. USA, pp.9273-9277, 1989.
DOI : 10.1073/pnas.86.23.9273
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC298476/pdf

Y. T. Wang, W. J. Yang, C. L. Li, L. G. Doudeva, and H. S. Yuan, Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases, Nucleic Acids Research, vol.35, issue.2, pp.584-594, 2007.
DOI : 10.1093/nar/gkl621
URL : http://doi.org/10.1093/nar/gkl621

B. Heddi, N. Foloppe, N. Bouchemal, E. Hantz, and B. Hartmann, Quantification of DNA BI/BII Backbone States in Solution. Implications for DNA Overall Structure and Recognition, Journal of the American Chemical Society, vol.128, issue.28, pp.9170-9177, 2006.
DOI : 10.1021/ja061686j

B. Heddi, N. Foloppe, E. Hantz, and B. Hartmann, The DNA Structure Responds Differently to Physiological Concentrations of K+ or Na+, Journal of Molecular Biology, vol.368, issue.5, pp.1403-1411, 2007.
DOI : 10.1016/j.jmb.2007.03.010
URL : https://hal.archives-ouvertes.fr/hal-00609952

A. V. Fratini, M. L. Kopka, H. R. Drew, and R. E. Dickerson, Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG, J. Biol. Chem, vol.257, pp.14686-14707, 1982.

D. G. Gorenstein, Phosphorus-31 NMR: Principles and Applications Academic Press, 1984.

D. G. Gorenstein, Conformation and Dynamics of DNA and Protein-DNA Complexes by 31P NMR, Chemical Reviews, vol.94, issue.5, pp.1315-1358, 1994.
DOI : 10.1021/cr00029a007

D. Djuranovic and B. Hartmann, Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states, Journal of Biomolecular Structure and Dynamics, vol.16, issue.6, pp.771-788, 2003.
DOI : 10.1080/07391102.1998.10508269

R. J. Isaacs and H. P. Spielmann, NMR evidence for mechanical coupling of phosphate BI-BII transitions with deoxyribose conformational exchange in DNA, Journal of Molecular Biology, vol.311, issue.1, pp.149-160, 2001.
DOI : 10.1006/jmbi.2001.4855

D. Djuranovic and B. Hartmann, DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations, Biopolymers, vol.391, issue.3, pp.356-368, 2004.
DOI : 10.1080/07391102.1998.10508269

B. Hartmann, D. Piazzola, and R. Lavery, transitions in B-DNA, Nucleic Acids Research, vol.21, issue.3, pp.561-568, 1993.
DOI : 10.1093/nar/21.3.561
URL : https://hal.archives-ouvertes.fr/hal-00313436

B. Heddi, N. Foloppe, C. Oguey, and B. Hartmann, Importance of Accurate DNA Structures in Solution: The Jun???Fos Model, Journal of Molecular Biology, vol.382, issue.4, pp.956-970, 2008.
DOI : 10.1016/j.jmb.2008.07.047

A. R. Srinivasan and W. K. Olson, Nucleic Acid Model Building: The Multiple Backbone Solutions Associated with a Given Base Morphology, Journal of Biomolecular Structure and Dynamics, vol.2, issue.6, pp.895-938, 1987.
DOI : 10.1016/S0022-2836(77)80200-3

L. Van-dam and M. H. Levitt, BII Nucleotides in the B and C Forms of Natural-sequence Polymeric DNA: A New Model for the C Form of DNA, Journal of Molecular Biology, vol.304, issue.4, pp.541-561, 2000.
DOI : 10.1006/jmbi.2000.4194

R. H. Winger, K. R. Liedl, A. Pichler, A. Hallbrucker, and E. Mayer, Substate Interconversion, Journal of Biomolecular Structure and Dynamics, vol.5, issue.2, pp.223-235, 1999.
DOI : 10.1007/978-1-4612-5190-3

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

W. K. Olson, A. A. Gorin, X. J. Lu, L. M. Hock, and V. B. Zhurkin, DNA sequence-dependent deformability deduced from protein-DNA crystal complexes, Proc. Natl Acad. Sci. USA, pp.11163-11168, 1998.
DOI : 10.1006/jmbi.1997.0916
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC21613/pdf

D. Djuranovic and B. Hartmann, Molecular Dynamics Studies on Free and Bound Targets of the Bovine Papillomavirus Type I E2 Protein: The Protein Binding Effect on DNA and the Recognition Mechanism, Biophysical Journal, vol.89, issue.4, pp.2542-2551, 2005.
DOI : 10.1529/biophysj.104.057109

B. Hartmann, M. R. Sullivan, and L. F. Harris, Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50-bp DNA reveal important differences between the OR1 and OR2 sites, Biopolymers, vol.77, issue.2, pp.250-264, 2003.
DOI : 10.1002/bip.10243

D. B. Huang, C. B. Phelps, A. J. Fusco, and G. Ghosh, Crystal Structure of a Free ??B DNA: Insights into DNA Recognition by Transcription Factor NF-??B, Journal of Molecular Biology, vol.346, issue.1, pp.147-160, 2005.
DOI : 10.1016/j.jmb.2004.11.042

S. Y. Reddy, S. Obika, and T. C. Bruice, Conformations and dynamics of Ets-1 ETS domain-DNA complexes, Proc. Natl Acad. Sci. USA, pp.15475-15480, 2003.
DOI : 10.1006/jmbi.2001.5090
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307592

C. Tisne, M. Delepierre, and B. Hartmann, How NF-??B can be attracted by its cognate DNA, Journal of Molecular Biology, vol.293, issue.1, pp.139-150, 1999.
DOI : 10.1006/jmbi.1999.3157

C. Tisne, E. Hantz, B. Hartmann, and M. Delepierre, Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 ??b site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex 1 1Edited by I. Tinoco, Journal of Molecular Biology, vol.279, issue.1, pp.127-142, 1998.
DOI : 10.1006/jmbi.1998.1757

V. W. Campbell and D. A. Jackson, The effect of divalent cations on the mode of action of DNase I. The initial reaction products produced from covalently closed circular DNA, J. Biol. Chem, vol.255, pp.3726-3735, 1980.

H. Bertrand, T. Ha-duong, S. Fermandjian, and B. Hartmann, Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps, Nucleic Acids Research, vol.26, issue.5, pp.1261-1267, 1998.
DOI : 10.1093/nar/26.5.1261

S. Neugebauerova and J. Kypr, Invariant and Variable Base Stacking Geometries in B-DNA and A-DNA, Journal of Biomolecular Structure and Dynamics, vol.169, issue.1, pp.73-81, 2000.
DOI : 10.1021/ja960459m

J. Sponer, J. Florian, H. L. Ng, J. E. Sponer, and N. Packova, Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B ? A intermediate crystal structure, Nucleic Acids Res, vol.28, pp.4893-4902, 2000.

T. K. Chiu and R. E. Dickerson, 1 ?? crystal structures of B -DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium 1 1Edited by I. Tinoco, Journal of Molecular Biology, vol.301, issue.4, pp.915-945, 2000.
DOI : 10.1006/jmbi.2000.4012

D. A. Case, T. E. Cheatham, . Iii, T. Darden, H. Gohlke et al., The Amber biomolecular simulation programs, Journal of Computational Chemistry, vol.124, issue.16, pp.1668-1688, 2005.
DOI : 10.1021/j100785a001
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1989667

T. E. Cheatham, . Iii, 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 : 10.1080/07391102.1998.10508245

E. Stofer and R. Lavery, Measuring the geometry of DNA grooves, Biopolymers, vol.6, issue.3, pp.337-346, 1994.
DOI : 10.1080/07391102.1989.10507729
URL : https://hal.archives-ouvertes.fr/hal-00313430

R. Lavery and B. Pullman, The molecular electrostatic potential, steric accessibility and hydration of Dickerson's B-DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG), Nucleic Acids Research, vol.9, issue.15, pp.3765-3777, 1981.
DOI : 10.1093/nar/9.15.3765