Thermodynamics of 5-Bromouracil Tautomerization From First-Principles Molecular Dynamics Simulations

The authors acknowledge support from the Engineering and Physical Sciences Research Council (EPSRC) UK National Service for Computational Chemistry Software (NSCCS); from GENCI (Grand equipement national de calcul intensif); and from CINES (Centre informatique national de l’enseignement superieur). LFH and TvM gratefully acknowledge support from the HPC-EUROPA2 project with the support of the European Commission - Capacities Area - Research Infrastructures. LFH is grateful to the EPSRC for studentship support through the Doctoral Training Account scheme (grant code EP/K503162/1).

[1]  F. Crick,et al.  The structure of DNA. , 1953, Cold Spring Harbor symposia on quantitative biology.

[2]  Marie-Pierre Gaigeot,et al.  Proton transfer from the inactive gas-phase nicotine structure to the bioactive aqueous-phase structure. , 2010, Journal of the American Chemical Society.

[3]  A. Katritzky,et al.  299. Tautomeric azines. Part I. The tautomerism of 1-methyluracil and 5-bromo-1-methyluracil , 1962 .

[4]  Donald G. Truhlar,et al.  The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06 functionals and 12 other functionals , 2008 .

[5]  M. A. Palafox,et al.  Tautomerism in 5-Bromouracil: Relationships with Other 5-Haloderivatives and Effect of the Microhydration , 2011 .

[6]  G. Streisinger,et al.  THE MECHANISM OF 5-BROMOURACIL MUTAGENESIS IN THE BACTERIOPHAGE T4 , 1962 .

[7]  D. Wemmer,et al.  NMR evidence for DNA bound water in solution , 1992 .

[8]  J. R. Fresco,et al.  Identification by UV resonance Raman spectroscopy of an imino tautomer of 5-hydroxy-2'-deoxycytidine, a powerful base analog transition mutagen with a much higher unfavored tautomer frequency than that of the natural residue 2'-deoxycytidine. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Xingbang Hu,et al.  Systematic study of the tautomerism of uracil induced by proton transfer. Exploration of water stabilization and mutagenicity. , 2005, The journal of physical chemistry. B.

[10]  Effect of hydration on the stability and tautomerisms of different isomers of uracil , 2014 .

[11]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[12]  Jürg Hutter,et al.  Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods , 2009 .

[13]  T. H. Dunning Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[14]  T. Dunning,et al.  Electron affinities of the first‐row atoms revisited. Systematic basis sets and wave functions , 1992 .

[15]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[16]  Frank Neese,et al.  The ORCA program system , 2012 .

[17]  T. Tsukamoto,et al.  A DFT study of uracil and 5-bromouracil in nanodroplets , 2010 .

[18]  F. J. Luque,et al.  TAUTOMERISM OF 1-METHYL DERIVATIVES OF URACIL, THYMINE, AND 5-BROMOURACIL.IS TAUTOMERISM THE BASIS FOR THE MUTAGENICITY OF 5-BROMOURIDINE? , 1998 .

[19]  De-jie Li,et al.  Catalysis effects of water molecules and of charge on intramolecular proton transfer of uracil. , 2009, The journal of physical chemistry. B.

[20]  D. Hovorun,et al.  How many tautomerization pathways connect Watson–Crick-like G*·T DNA base mispair and wobble mismatches? , 2015, Journal of biomolecular structure & dynamics.

[21]  S. Zamenhof,et al.  Incorporation of Halogenated Pyrimidines into the Deoxyribonucleic Acids of Bacterium Coli and its Bacteriophages , 1954, Nature.

[22]  Frederic Lawrence Holmes,et al.  Meselson, Stahl, and the Replication of DNA: A History of 'The Most Beautiful Experiment in Biology' , 2001 .

[23]  R. Davidson,et al.  DNA base sequence changes and sequence specificity of bromodeoxyuridine-induced mutations in mammalian cells. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Jeehiun K. Lee,et al.  The acidity of uracil and uracil analogs in the gas phase: Four surprisingly acidic sites and biological implications , 2002, Journal of the American Society for Mass Spectrometry.

[25]  W. Hunter,et al.  Structural characterisation of the bromouracil.guanine base pair mismatch in a Z-DNA fragment. , 1986, Nucleic acids research.

[26]  T. Tsukamoto,et al.  On the mechanism of the mutagenic action of 5-bromouracil: a DFT study of uracil and 5-bromouracil in a water cluster. , 2009, The journal of physical chemistry. A.

[27]  E. Kool,et al.  Difluorotoluene, a Nonpolar Isostere for Thymine, Codes Specifically and Efficiently for Adenine in DNA Replication. , 1997, Journal of the American Chemical Society.

[28]  M. Gaigeot,et al.  Ab Initio Molecular Dynamics Computation of the Infrared Spectrum of Aqueous Uracil , 2003 .

[29]  M. Klein,et al.  Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics. , 2002, Journal of the American Chemical Society.

[30]  H. Al‐Hashimi,et al.  Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs. , 2017, Journal of the American Chemical Society.

[31]  Walter Thiel,et al.  Enzymatic Hydroxylation in p-Hydroxybenzoate Hydroxylase:  A Case Study for QM/MM Molecular Dynamics. , 2005, Journal of chemical theory and computation.

[32]  J. Tomasi,et al.  Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .

[33]  Maciej Gutowski,et al.  Stabilization of very rare tautomers of uracil by an excess electron. , 2005, Physical chemistry chemical physics : PCCP.

[34]  A. Klamt,et al.  COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .

[35]  T. Kunkel,et al.  Fidelity of DNA synthesis. , 1982, Annual review of biochemistry.

[36]  E. Freese The specific mutagenic effect of base analogues on Phage T4 , 1959 .

[37]  Gregory A Voth,et al.  Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited. , 2005, The Journal of chemical physics.

[38]  D. Hovorun,et al.  The nature of the transition mismatches with Watson–Crick architecture: the G*·T or G·T* DNA base mispair or both? A QM/QTAIM perspective for the biological problem , 2015, Journal of biomolecular structure & dynamics.

[39]  Leonard Kleinman,et al.  Efficacious Form for Model Pseudopotentials , 1982 .

[40]  S. Grimme Improved second-order Møller–Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies , 2003 .

[41]  M. Bühl,et al.  Structure of a uranyl peroxo complex in aqueous solution from first-principles molecular dynamics simulations. , 2014, Dalton transactions.

[42]  W. Goddard,et al.  First Principles Calculation of pKa Values for 5-Substituted Uracils , 2001 .

[43]  M. Gaigeot Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase. , 2010, Physical chemistry chemical physics : PCCP.

[44]  R. Eritja,et al.  Ionized and wobble base-pairing for bromouracil-guanine in equilibrium under physiological conditions. A nuclear magnetic resonance study on an oligonucleotide containing a bromouracil-guanine base-pair as a function of pH. , 1989, Journal of molecular biology.

[45]  M. Alcamí,et al.  Ultrafast damage following radiation-induced oxidation of uracil in aqueous solution. , 2013, Angewandte Chemie.

[46]  D. Nachtigallová,et al.  Mutagenic properties of 5-halogenuracils: correlated quantum chemical ab initio study. , 2005, Biochemistry.

[47]  M. Sprik Computation of the pK of liquid water using coordination constraints , 2000 .

[48]  E. Kimura,et al.  Facile and Selective Electrostatic Stabilization of Uracil N(1)- Anion by a Proximate Protonated Amine: A Chemical Implication for Why Uracil N(1) Is Chosen for Glycosylation Site , 1997 .

[49]  D. Wood,et al.  M-DNA is stabilised in G*C tracts or by incorporation of 5-fluorouracil. , 2002, Nucleic acids research.

[50]  Teodora Todorova,et al.  Molecular dynamics simulation of liquid water: hybrid density functionals. , 2006, The journal of physical chemistry. B.

[51]  O. Isayev,et al.  Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration. , 2011, Physical chemistry chemical physics : PCCP.

[52]  D. Truhlar,et al.  The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .

[53]  Hülya Yekeler,et al.  Concerning the solvent effect in the tautomerism of uracil, 5-fluorouracil, and thymine by density-functional theory and ab initio calculations , 2001 .

[54]  Xingbang Hu,et al.  Tautomerism of uracil and 5-bromouracil in a microcosmic environment with water and metal ions. What roles do metal ions play? , 2007, The journal of physical chemistry. B.

[55]  H. Adams,et al.  The effect of tautomeric constant on the specificity of nucleotide incorporation during DNA replication: support for the rare tautomer hypothesis of substitution mutagenesis. , 2003, Journal of molecular biology.

[56]  H. Al‐Hashimi,et al.  Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes , 2015, Nature.

[57]  Stefan Grimme,et al.  Accurate description of van der Waals complexes by density functional theory including empirical corrections , 2004, J. Comput. Chem..

[58]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[59]  D. Hovorun,et al.  Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding , 2012 .

[60]  Martins,et al.  Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.

[61]  Axel D. Becke,et al.  Density-functional thermochemistry. I. The effect of the exchange-only gradient correction , 1992 .

[62]  M. D. Topal,et al.  Complementary base pairing and the origin of substitution mutations , 1976, Nature.

[63]  Michiel Sprik,et al.  Free energy from constrained molecular dynamics , 1998 .

[64]  I. Timtcheva,et al.  Oxo-hydroxy tautomerism of 5-fluorouracil: water-assisted proton transfer. , 2005, The journal of physical chemistry. A.