D. Rhodes and H. J. Lipps, G-quadruplexes and their regulatory roles in biology, Nucleic Acids Research, vol.43, issue.18, pp.43-8627
DOI : 10.1093/nar/gkv862
URL : http://doi.org/10.1093/nar/gkv862

J. R. Williamson, G-Quartet Structures in Telomeric DNA, Annual Review of Biophysics and Biomolecular Structure, vol.23, issue.1, pp.703-730, 1994.
DOI : 10.1146/annurev.bb.23.060194.003415

T. Oelschlaegel, B. Xhemalce, S. Balasubramanian, and S. P. Jackson, Small Molecule-Induced DNA Damage Identifies Alternative DNA Structures in Human Genes, Nature chemical biology, vol.2012, issue.83, pp.301-310

G. Biffi, D. Tannahill, J. Mccafferty, and S. Balasubramanian, Quantitative visualization of DNA G-quadruplex structures in human cells, Nature Chemistry, vol.3, issue.3, pp.182-186, 2013.
DOI : 10.1038/nchem.1548

A. Siddiqui-jain, C. L. Grand, D. J. Bearss, and L. H. Hurley, Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription, Proceedings of the National Academy of Sciences, vol.281, issue.5382, pp.99-11593, 2002.
DOI : 10.1126/science.281.5382.1509

T. S. Dexheimer, D. Sun, and L. H. Hurley, Deconvoluting the Structural and Drug- Recognition Complexity of the G-Quadruplex-Forming Region Upstream of the bcl-2 P1 Promoter, Journal of the American Chemical Society, issue.16, pp.128-5404, 2006.

D. Wei, G. N. Parkinson, A. P. Reszka, and S. Neidle, Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation, Nucleic Acids Research, vol.40, issue.10, pp.40-4691
DOI : 10.1093/nar/gks023

P. Agrawal, E. Hatzakis, K. Guo, M. Carver, and D. Yang, Solution structure of the major G-quadruplex formed in the human VEGF promoter in K+: insights into loop interactions of the parallel G-quadruplexes, Nucleic Acids Research, vol.41, issue.22, pp.41-10584
DOI : 10.1093/nar/gkt784

M. Métifiot, S. Amrane, S. Litvak, and M. Andreola, G-quadruplexes in viruses: function and potential therapeutic applications, Nucleic Acids Research, vol.42, issue.20, pp.42-12352
DOI : 10.1093/nar/gku999

S. Amrane, A. Kerkour, A. Bedrat, B. Vialet, M. Andreola et al., Topology of a DNA G-Quadruplex Structure Formed in the HIV-1 Promoter: A Potential Target for Anti-HIV Drug Development, Journal of the American Chemical Society, vol.136, issue.14, pp.136-5249
DOI : 10.1021/ja501500c
URL : https://hal.archives-ouvertes.fr/hal-01101069

F. Moraca, G. Costa, F. Ortuso, E. Maccioni, and C. Sissi, Identification and Characterization of New DNA G-Quadruplex Binders Selected by a Combination of Ligand and Structure- Based Virtual Screening Approaches, Journal of Medicinal Chemistry, vol.2013, issue.12, pp.843-855

A. David, J. Lehn, and W. D. Wilson, Selective Recognition of G-Quadruplex Telomeric DNA by a Bis(quinacridine) Macrocycle, Journal of the American Chemical Society Z.; Fakhoury, J N, vol.125, issue.16, pp.4732-4740, 2003.

H. F. Sleiman, L. H. Hurley, and S. Neidle, II) Phenylphenanthroimidazole with an Extended Side-Chain Exhibits Slow Dissociation from a c-Kit G-Quadruplex Motif Targeting G-Quadruplexes in Gene Promoters: a Novel Anticancer Strategy? Nature reviews. Drug discovery, Chemistry. A European Journal Balasubramanian, S J.-L, vol.2013, issue.15, pp.17836-17845, 2011.

H. Sugiyama, Small Molecule Binding to a G-Hairpin and a G-Triplex: a New Insight into Anticancer Drug Design Targeting G-Rich Regions, Chemical Communications, vol.2015, issue.16, pp.9181-9184

E. Penzo, S. J. Wind, R. Di-felice, and S. S. Skourtis, Long-Range Charge Transport in Single G-Quadruplex DNA Molecules Programmed Self-Assembly of a Quadruplex DNA Nanowire Nucleic Acid G-Quartets: Insights into Diverse Patterns and Optical Properties, Nat Nano Chemistry. A European Journal The Journal of Physical Chemistry C, vol.2014, issue.18, pp.1040-1046, 2011.

D. Zikich, P. ?ket, J. Plavec, D. E. Markovitsi, and A. Erbe, Cation Effect on the Electronic Excited States of Guanine Nanostructures Studied by Time-Resolved Fluorescence Spectroscopy Direct Measurement of Electrical Transport Through G-Quadruplex DNA with Mechanically Controllable Break Junction Electrodes, The Journal of Physical Chemistry C Angewandte Chemie International Edition, vol.2012, issue.20, pp.14682-14689, 2010.

M. Trajkovski and J. Plavec, Assessing Roles of Cations in G-Quadruplex-Based Nanowires by NMR, The Journal of Physical Chemistry C, vol.116, issue.44, pp.23821-23825
DOI : 10.1021/jp308824j

G. N. Parkinson, M. P. Lee, and S. Neidle, Crystal structure of parallel quadruplexes from human telomeric DNA, Nature, vol.5, issue.6891, pp.417-876, 2002.
DOI : 10.1038/nature755

S. Bouaziz, A. Kettani, D. J. Patel, A. Dna-quadruplex-containing, G. Lim et al., Cation-Induced Conformational Switch within a Loop Spanning Segment of a Structure of the Human Telomere in K(+) Solution: a Stable Basket-Type G- Quadruplex with only two G-Tetrad Layers Structural Basis of DNA Quadruplex Recognition by an Acridine Drug, Journal of Molecular Biology Journal of the American Chemical Society Journal of the American Chemical Society, vol.282, issue.2521, pp.637-652, 1998.

P. Agrawal, C. Lin, R. I. Mathad, M. Carver, D. Yang et al., Solution, Journal of the American Chemical Society, vol.136, issue.5, pp.1750-1753, 2002.
DOI : 10.1021/ja4118945
URL : https://hal.archives-ouvertes.fr/lirmm-01162359

T. Kulinski, J. ?poner, B. Islam, P. Stadlbauer, M. Krepl et al., Extended Molecular Dynamics of a c-kit Promoter Quadruplex Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes, Journal of Chemical Theory and Computation Nucleic Acids Research Journal of Chemical Theory and Computation, vol.5, issue.1212, pp.2514-2530, 2009.

S. Neidle, M. Otyepka, S. Bazzi, J. Novotný, Y. P. Yurenko et al., An Overview from MD Simulation StudiesGeneral Subjects, in press Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands The Role of Alkali Metal Cations in the Stabilization of Guanine Quadruplexes: why K+ is the Best, Folding of Guanine Quadruplex Molecules?Funnel-Like Mechanism or Kinetic Partitioning Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations Telomere Structure and Stability: Covalency in Hydrogen Bonds, Not Resonance Assistance, Causes Cooperativity in Guanine Quartets, pp.9414-9425, 2011.

G. Paragi and C. Fonseca-guerra, Cooperativity in the Self-Assembly of the Guanine Nucleobase into Quartet and Ribbon Structures on Surfaces, Chemistry - A European Journal, vol.12, issue.13, pp.3042-3050, 2017.
DOI : 10.1002/chem.201604830

K. Gkionis, H. Kruse, J. A. Platts, A. Mládek, J. Ko?a et al., Ion Binding to Quadruplex DNA Stems Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5'-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA Anisotropic, Polarizable Molecular Mechanics Studies of Inter-and Intramolecular Interactions and Ligand?Macromolecule Complexes. A Bottom-Up Strategy Quantum- Chemistry Based Calibration of the Alkali Metal Cation Series (Li+-Cs+) for Large-Scale Polarizable Molecular Mechanics/Dynamics Simulations, Journal of Chemical Theory and Computation The Journal of Physical Chemistry B Journal of Chemical Theory and Computation Dudev, T Journal of Computational Chemistry Gresh, N.; Sponer, J. E.; Devereux, M B J.-P, vol.2014, issue.365, pp.1326-1340, 2003.

J. Sponer, H. Stacked, B. Pullman, J. Dunning, T. H. Feller et al., A Theoretical study of the Selective Entrapment of Alkali and Ammonium Cations Between Guanine Tetramers Gaussian Basis Sets for Use in Correlated Molecular Calculations. I. The atoms boron through neon and hydrogen. The Journal of Chemical Physics The Role of Data Bases in Support of Computational Chemistry Calculations Gaussian Basis Set of Triple Zeta Valence Quality for the Atoms from K to Kr: Application in DFT and CCSD(T) Calculations of Molecular Properties Ab Initio Energy-Adjusted Pseudopotentials for Elements of Groups 13?17, Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics Frozen Fragment Reduced Variational Space Analysis of Hydrogen Bonding Interactions. Application to the Water Dimer, pp.9477-9495, 1986.

J. A. Montgomery, General Atomic and Molecular Electronic Structure System, Journal of Computational Chemistry, vol.14, issue.11, pp.1347-1363, 1993.

S. Grimme, J. Antony, S. Ehrlich, H. Krieg, and R. G. Parr, A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H- Pu Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density, 154104. 50. Lee, pp.785-789, 1988.

A. D. Becke, A new mixing of Hartree???Fock and local density???functional theories, The Journal of Chemical Physics, vol.23, issue.2
DOI : 10.1103/PhysRevA.38.3098

A. J. Stone, J. Piquemal, N. Gresh, C. Giessner-prettre, H. Chevreau et al., Distributed multipole analysis, Toward a Separate Reproduction of the Contributions to the Hartree?Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential, pp.1128-1132, 2003.
DOI : 10.1080/00268978500102891

D. R. Garmer and W. J. Stevens, How Closely Can a Separable, ab Initio-Grounded Molecular Mechanics Procedure Reproduce the Results of Supermolecule Quantum Chemical Computations? The Journal of Physical Chemistry A Adjustment of the SIBFA Method for Potential Maps to Study Hydrogen Bonding Vibrational Frequencies A Supervised Fitting Approach to Force Field Parametrization with Application to the SIBFA Polarizable Force Field, Hutson, J. M., I-NoLLS: A Program for Interactive Nonlinear Least- Squares Fitting of the Parameters of Physical Models. Computer Physics Communications, pp.8263-8270, 1989.

W. Yang and J. Contreras-garcía, Revealing Non-Covalent Interactions, Journal of the American Chemical Society E. R.; Keinan, S.; Chaudret, R.; Piquemal, J.-P, vol.132, issue.62, pp.6498-6506, 2010.

D. N. Beratan, W. Yang, A. J. Misquitta, A. J. Stone, F. Fazeli et al., Distributed Multipoles from a Robust Basis- Space Implementation of the Iterated Stockholder Atoms Procedure Atomic Charge Densities Generated Using an Iterative Stockholder Procedure, 144101. 65. Elking 66. Cisneros, G. A., Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field, pp.625-632, 2009.

E. Hage, K. Piquemal, J. Hobaika, Z. Maroun, R. G. Gresh et al., Substituent- Modulated Affinities of Halobenzene Derivatives to the HIV-1 Integrase Recognition Site Analyses of the Interaction Energies by Parallel Quantum Chemical and Polarizable Molecular Mechanics. The Journal of Physical Chemistry A Complexes of a Zn-Metalloenzyme Binding Site with Hydroxamate- Containing Ligands. A Case for Detailed Benchmarkings of Polarizable Molecular Mechanics/Dynamics Potentials when the Experimental Binding Structure is Unknown, Journal of Computational Chemistry J. D, vol.118, issue.3732, pp.9772-9782, 2014.

I. Haque, D. L. Mobley, D. S. Lambrecht, and R. A. Distasio, Current Status of the AMOEBA Polarizable Force Field Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model, The Journal of Physical Chemistry B Journal of Chemical Theory and Computation The Journal of Physical Chemistry B, vol.114, issue.12044, pp.2549-2564, 2010.

A. D. Mackerell and B. Roux, Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator, Journal of Chemical Theory and Computation, vol.2, issue.6, pp.1587-1597, 2006.

T. Hp_team, G. Tinker-hp-jansen, and A. Hesselmann, Accessed Comment on " Using Kohn?Sham Orbitals in Symmetry- Adapted Perturbation Theory To Investigate Intermolecular Interactions, The Journal of Physical Chemistry A, issue.49, pp.105-11156, 2001.

B. Jeziorski, R. Moszynski, and K. Szalewicz, Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes, Chemical Reviews, vol.94, issue.7, pp.1887-1930, 1994.
DOI : 10.1021/cr00031a008