M. Helm and J. D. Alfonzo, Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell???s Chemical Legoland, Chemistry & Biology, vol.21, issue.2, p.174, 2014.
DOI : 10.1016/j.chembiol.2013.10.015

B. T. Thole, Molecular polarizabilities calculated with a modified dipole interaction, Chemical Physics, vol.59, issue.3, p.341, 1981.
DOI : 10.1016/0301-0104(81)85176-2

M. Helm, Post-transcriptional nucleotide modification and alternative folding of RNA, Nucleic Acids Research, vol.34, issue.2, p.721, 2006.
DOI : 10.1093/nar/gkj471

K. N. Nobles, C. S. Yarian, G. Liu, R. H. Guenther, and P. F. Agris, Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding, Nucleic Acids Research, vol.30, issue.21, p.4751, 2002.
DOI : 10.1093/nar/gkf595
URL : http://doi.org/10.1093/nar/gkf595

D. Hirsh, Tryptophan transfer RNA as the UGA suppressor, Journal of Molecular Biology, vol.58, issue.2, p.439, 1971.
DOI : 10.1016/0022-2836(71)90362-7

T. M. Schmeing, R. M. Voorhees, A. C. Kelley, and V. Ramakrishnan, How mutations in tRNA distant from the anticodon affect the fidelity of decoding, Nature Structural & Molecular Biology, vol.254, issue.4, p.432, 2011.
DOI : 10.1107/S0907444998003254

B. R. Brooks, C. L. Brooks, A. D. Iii, J. Mackerell, L. Nilsson et al., CHARMM: The biomolecular simulation program, Journal of Computational Chemistry, vol.103, issue.13, p.1545, 2009.
DOI : 10.1002/jcc.21287

M. Karplus and R. Lavery, Significance of Molecular Dynamics Simulations for Life Sciences, Israel Journal of Chemistry, vol.107, issue.8-9, p.1042, 2014.
DOI : 10.1002/ijch.201400074

R. N. Witts, E. C. Hopson, D. E. Koballa, T. A. Van-boening, N. H. Hopkins et al., Backbone???Base Interactions Critical to Quantum Stabilization of Transfer RNA Anticodon Structure, The Journal of Physical Chemistry B, vol.117, issue.25, pp.7489-3473, 2013.
DOI : 10.1021/jp400084p

W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz et al., , 5179???5197, Journal of the American Chemical Society, vol.118, issue.9, p.2309, 1996.
DOI : 10.1021/ja955032e

V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg et al., Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins: Structure, Function, and Bioinformatics, vol.43, issue.3, p.712, 2006.
DOI : 10.1002/prot.21123

W. L. Jorgensen and J. Tiradorives, The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin, Journal of the American Chemical Society, vol.110, issue.6, p.1657, 1988.
DOI : 10.1021/ja00214a001

N. Foloppe and A. D. , All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data, Journal of Computational Chemistry, vol.7, issue.2, p.86, 2000.
DOI : 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G

K. Hart, N. Foloppe, C. M. Baker, E. J. Denning, L. Nilsson et al., Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium, Journal of Chemical Theory and Computation, vol.8, issue.1, p.348, 2012.
DOI : 10.1021/ct200723y

J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O-'connor, D. J. Tobias et al., Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types, The Journal of Physical Chemistry B, vol.114, issue.23, p.7830, 2010.
DOI : 10.1021/jp101759q

C. J. Dickson, B. D. Madej, A. A. Skjevik, R. M. Betz, K. Teigen et al., Lipid14: The Amber Lipid Force Field, Journal of Chemical Theory and Computation, vol.10, issue.2, p.865, 2014.
DOI : 10.1021/ct4010307

X. Daura, A. E. Mark, and W. F. Van-gunsteren, Parametrization of aliphatic CHn united atoms of GROMOS96 force field, Journal of Computational Chemistry, vol.81, issue.5, p.535, 1998.
DOI : 10.1002/(SICI)1096-987X(19980415)19:5<535::AID-JCC6>3.0.CO;2-N

W. L. Jorgensen, D. S. Maxwell, and J. Tiradorives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, Journal of the American Chemical Society, vol.118, issue.45, p.11225, 1996.
DOI : 10.1021/ja9621760

W. Press, ;. B. Flannery, S. Teukolsky-;-w, and . Vetterling, Numerical Recipes, 1986.

A. P. Scott and L. Radom, Harmonic Vibrational Frequencies:?? An Evaluation of Hartree???Fock, M??ller???Plesset, Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors, The Journal of Physical Chemistry, vol.100, issue.41, p.16502, 1996.
DOI : 10.1021/jp960976r

K. Kuczera, ;. K. Wiorkiewicz, and ;. Karplus, MOLVIB: Program for the Analysis of Molecular Vibrations, 2016.

J. P. Ryckaert, G. Ciccotti, and H. J. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, Journal of Computational Physics, vol.23, issue.3, p.327, 1977.
DOI : 10.1016/0021-9991(77)90098-5

N. Foloppe and L. Nilsson, Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution:?? Simulations of Nucleosides, The Journal of Physical Chemistry B, vol.109, issue.18, p.9119, 2005.
DOI : 10.1021/jp044513u

V. A. Bloomfield, D. M. Crothers, and J. I. Tinoco, Nucleic Acids: Structures , Properties, and Functions, 2000.

J. Florian, J. Sponer, and A. , Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution:?? Ab Initio/Langevin Dipoles Study, The Journal of Physical Chemistry B, vol.103, issue.5, p.884, 1999.
DOI : 10.1021/jp983699s

D. X. Yin and A. D. , Combinedab initio/empirical approach for optimization of Lennard-Jones parameters, Journal of Computational Chemistry, vol.107, issue.3, p.334, 1998.
DOI : 10.1002/(SICI)1096-987X(199802)19:3<334::AID-JCC7>3.0.CO;2-U

N. Foloppe, B. Hartmann, L. Nilsson, and A. D. , Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: A Quantum Mechanical Study, Biophysical Journal, vol.82, issue.3, p.1554, 2002.
DOI : 10.1016/S0006-3495(02)75507-0

N. Foloppe and A. D. , Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics, The Journal of Physical Chemistry B, vol.103, issue.49, p.10955, 1999.
DOI : 10.1021/jp992716q

E. Egert, H. J. Lindner, W. Hillen, and M. C. Bohm, Influence of substituents at the 5 position on the structure of uridine, Journal of the American Chemical Society, vol.102, issue.11, p.3707, 1980.
DOI : 10.1021/ja00531a007

N. Foloppe, A. D. Mackerell, and J. , Intrinsic Conformational Properties of Deoxyribonucleosides: Implicated Role for Cytosine in the Equilibrium Among the A, B, and Z Forms of DNA, Biophysical Journal, vol.76, issue.6, p.3206, 1999.
DOI : 10.1016/S0006-3495(99)77472-2

D. Suck and ;. W. Saenger, Molecular and crystal structure of the tRNA minor constituent dihydrouridine, Acta Crystallographica Section B, vol.28, issue.2, p.596, 1972.
DOI : 10.1107/S056774087200281X

D. R. Davis, Stabilization of RNA stacking by pseudouridine, Nucleic Acids Research, vol.23, issue.24, p.5020, 1995.
DOI : 10.1093/nar/23.24.5020

P. C. Durant and D. R. Davis, Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine, Journal of Molecular Biology, vol.285, issue.1, p.115, 1999.
DOI : 10.1006/jmbi.1998.2297

C. S. Yarian, M. M. Basti, R. J. Cain, G. Ansari, R. H. Guenther et al., Structural and functional roles of the N1- and N3-protons of ?? at tRNA's position 39, Nucleic Acids Research, vol.27, issue.17, p.3543, 1999.
DOI : 10.1093/nar/27.17.3543

N. K. Kim, C. A. Theimer, J. R. Mitchell, K. Collins, and J. Feigon, Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA, Nucleic Acids Research, vol.38, issue.19, p.6746, 2010.
DOI : 10.1093/nar/gkq525

J. M. Neumann, J. M. Bernassau, M. Gueron, and S. Trandinh, Comparative Conformations of Uridine and Pseudouridine and Their Derivatives, European Journal of Biochemistry, vol.92, issue.2, p.457, 1980.
DOI : 10.1016/0022-5193(77)90083-2

J. P. Desaulniers, H. M. Chui, and C. S. Chow, Solution conformations of two naturally occurring RNA nucleosides: 3-Methyluridine and 3-methylpseudouridine, Bioorganic & Medicinal Chemistry, vol.13, issue.24, p.6777, 2005.
DOI : 10.1016/j.bmc.2005.07.061

Y. C. Chang, J. Herath, T. H. Wang, and C. S. Chow, Synthesis and solution conformation studies of 3-substituted uridine and pseudouridine derivatives, Bioorganic & Medicinal Chemistry, vol.16, issue.5, p.2676, 2008.
DOI : 10.1016/j.bmc.2007.11.039

J. G. Arnez and T. A. Steitz, Crystal Structure of Unmodified tRNAGln Complexed with Glutaminyl-tRNA Synthetase and ATP Suggests a Possible Role for Pseudo-Uridines in Stabilization of RNA Structure, Biochemistry, vol.33, issue.24, p.7560, 1994.
DOI : 10.1021/bi00190a008

E. D. Hickey, L. A. Weber, C. Baglioni, C. H. Kim, and R. H. Sarma, A relation between inhibition of protein synthesis and conformation of 5???-phosphorylated 7-methylguanosine derivatives, Journal of Molecular Biology, vol.109, issue.2, p.173, 1977.
DOI : 10.1016/S0022-2836(77)80027-2

E. Darzynkiewicz and H. Lonnberg, Base stacking of simple mRNA cap analogues, Biophysical Chemistry, vol.33, issue.3, p.289, 1989.
DOI : 10.1016/0301-4622(89)80030-4

J. Santalucia and D. H. Turner, Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics, Biochemistry, vol.32, issue.47, p.12612, 1993.
DOI : 10.1021/bi00210a009

D. M. Cheng and R. H. Sarma, Nuclear magnetic resonance study of the impact of ribose 2???-O-methylation on the aqueous solution conformation of cytidylyl-(3??? ??? 5???)-cytidine, Biopolymers, vol.40, issue.8, p.1687, 1977.
DOI : 10.1002/bip.1977.360160807

A. F. Drake, S. F. Mason, and A. R. Trim, Optical studies of the base-stacking properties of 2???-O-methylated dinucleoside monophosphates, Journal of Molecular Biology, vol.86, issue.4, p.727, 1974.
DOI : 10.1016/0022-2836(74)90349-0

H. Singh, M. H. Herbut, C. H. Lee, and R. H. Sarma, Conformational features of 2?-O-methyl-adenosylyl-adenosine, Biopolymers, vol.11, issue.11, p.2167, 1976.
DOI : 10.1002/bip.1976.360151106

J. Norberg and L. Nilsson, Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics, Biophysical Journal, vol.67, issue.2, p.812, 1994.
DOI : 10.1016/S0006-3495(94)80541-7

J. Norberg and L. Nilsson, Stacking Free Energy Profiles for All 16 Natural Ribodinucleoside Monophosphates in Aqueous Solution, Journal of the American Chemical Society, vol.117, issue.44, p.10832, 1995.
DOI : 10.1021/ja00149a006

S. Barbe and M. L. Bret, -Methyl Uridine Inserted in Duplexes, The Journal of Physical Chemistry A, vol.112, issue.5, p.989, 2008.
DOI : 10.1021/jp075777u
URL : https://hal.archives-ouvertes.fr/hal-00908910

R. Parthasarathy, S. L. Ginell, N. C. De, and G. B. Chheda, Conformation of N4-acetylcytidine, a modified nucleoside of tRNA, and stereochemistry of codon-anticodon interaction, Biochemical and Biophysical Research Communications, vol.83, issue.2, p.657, 1978.
DOI : 10.1016/0006-291X(78)91040-9

D. P. Zhou, C. P. Zhai, and X. P. Xuan, Molecular structure and vibrational spectra of N4-acetylcytosine, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol.112, p.139, 2013.
DOI : 10.1016/j.saa.2013.04.051

J. D. Engel and P. H. , Effects of methylation on the stability of nucleic acid conformations. Monomer level, Biochemistry, vol.13, issue.20, p.4143, 1974.
DOI : 10.1021/bi00717a013

A. R. Cervi, A. Guy, G. A. Leonard, R. Teoule, and W. N. Hunter, CG), Nucleic Acids Research, vol.21, issue.24, p.5623, 1993.
DOI : 10.1093/nar/21.24.5623