Tautomerism of Guanine Analogues
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
18-11851S
Grantová Agentura České Republiky - International
PubMed
31979043
PubMed Central
PMC7072560
DOI
10.3390/biom10020170
PII: biom10020170
Knihovny.cz E-zdroje
- Klíčová slova
- DFT calculations, NMR spectroscopy, nucleic acids, tautomerism,
- MeSH
- cytosin analogy a deriváty chemie MeSH
- dimerizace MeSH
- DNA chemie MeSH
- elektrony MeSH
- guanin chemie MeSH
- kvantová teorie MeSH
- magnetická rezonanční spektroskopie metody MeSH
- makromolekulární látky MeSH
- normální rozdělení MeSH
- reprodukovatelnost výsledků MeSH
- stereoizomerie MeSH
- termodynamika MeSH
- vodík chemie MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- cytosin MeSH
- DNA MeSH
- guanin MeSH
- isocytosine MeSH Prohlížeč
- makromolekulární látky MeSH
- vodík MeSH
Tautomerism of nucleic acid (NA) bases is a crucial factor for the maintenance and translation of genetic information in organisms. Only canonical tautomers of NA bases can form hydrogen-bonded complexes with their natural counterparts. On the other hand, rare tautomers of nucleobases have been proposed to be involved in processes catalysed by NA enzymes. Isocytosine, which can be considered as a structural fragment of guanine, is known to have two stable tautomers both in solution and solid states. The tautomer equilibrium of isocytosine contrasts with the remarkable stability of the canonical tautomer of guanine. This paper investigates the factors contributing to the stability of the canonical tautomer of guanine by a combination of NMR experiments and theoretical calculations. The electronic effects of substituents on the stability of the rare tautomers of isocytosine and guanine derivatives are studied by density functional theory (DFT) calculations. Selected derivatives are studied by variable-temperature NMR spectroscopy. Rare tautomers can be stabilised in solution by intermolecular hydrogen-bonding interactions with suitable partners. These intermolecular interactions give rise to characteristic signals in proton NMR spectra, which make it possible to undoubtedly confirm the presence of a rare tautomer.
Zobrazit více v PubMed
Watson J.D., Crick F.H.C. Molecular Structure of Nucleic Acids—A Structure for Deoxyribose Nucleic Acid. Nature. 1953;171:737–738. doi: 10.1038/171737a0. PubMed DOI
Watson J.D., Crick F.H.C. Genetical Implications of the Structure of Deoxyribonucleic Acid. Nature. 1953;171:964–967. doi: 10.1038/171964b0. PubMed DOI
Löwdin P.O. Proton Tunneling in DNA and Its Biological Implications. Rev. Mod. Phys. 1963;35:724–732. doi: 10.1103/RevModPhys.35.724. DOI
Pérez A., Tuckerman M.E., Hjalmarson H.P., von Lilienfeld O.A. Enol Tautomers of Watson-Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effects. J. Am. Chem. Soc. 2010;132:11510–11515. doi: 10.1021/ja102004b. PubMed DOI
Florián J., Leszczyński J. Spontaneous DNA mutations induced by proton transfer in the guanine cytosine base pairs: An energetic perspective. J. Am. Chem. Soc. 1996;118:3010–3017. doi: 10.1021/ja951983g. DOI
Singh V., Fedeles B., Essigmann J.M. Role of tautomerism in RNA biochemistry. RNA. 2017;21:1–13. doi: 10.1261/rna.048371.114. PubMed DOI PMC
Cochrane J.C., Strobel S.A. Catalytic strategies of self-cleaving ribozymes. Acc. Chem. Res. 2008;41:1027–1035. doi: 10.1021/ar800050c. PubMed DOI
Hanus M., Ryjáček F., Kabeláč M., Kubar T., Bogdan T.V., Trygubenko S.A., Hobza P. Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Guanine: Surprising stabilization of rare tautomers in aqueous solution. J. Am. Chem. Soc. 2003;125:7678–7688. doi: 10.1021/ja034245y. PubMed DOI
Dolgounitcheva O., Zakrzewski V.G., Ortiz J.V. Electron propagator theory of guanine and its cations: Tautomerism and photoelectron spectra. J. Am. Chem. Soc. 2000;122:12304–12309. doi: 10.1021/ja0015747. DOI
Colominas C., Luque F.J., Orozco M. Tautomerism and protonation of guanine and cytosine. Implications in the formation of hydrogen-bonded complexes. J. Am. Chem. Soc. 1996;118:6811–6821. doi: 10.1021/ja954293l. DOI
Stasyuk O.A., Szatylowicz H., Krygowski T.M. Effect of the H-Bonding on Aromaticity of Purine Tautomers. J. Org. Chem. 2012;77:4035–4045. doi: 10.1021/jo300406r. PubMed DOI
Marín-Luna M., Alkorta I., Elguero J. The influence of intermolecular halogen bonds on the tautomerism of nucleobases. I. Guanine. Tetrahedron. 2015;71:5260–5266. doi: 10.1016/j.tet.2015.06.023. DOI
Hobza P., Šponer J. Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chem. Rev. 1999;99:3247–3276. doi: 10.1021/cr9800255. PubMed DOI
Piuzzi F., Mons M., Dimicoli I., Tardivel B., Zhao Q. Ultraviolet spectroscopy and tautomerism of the DNA base guanine and its hydrate formed in a supersonic jet. Chem. Phys. 2001;270:205–214. doi: 10.1016/S0301-0104(01)00393-7. DOI
Mons M., Dimicoli I., Piuzzi F., Tardivel B., Elhanine M. Tautomerism of the DNA base guanine and its methylated derivatives as studied by gas-phase infrared and ultraviolet spectroscopy. J. Phys. Chem. A. 2002;106:5088–5094. doi: 10.1021/jp0139742. DOI
Li W., Jin J., Liu X.Q., Wang L. Structural Transformation of Guanine Coordination Motifs in Water Induced by Metal Ions and Temperature. Langmuir. 2018;34:8092–8098. doi: 10.1021/acs.langmuir.8b01263. PubMed DOI
Zhang C., Xie L., Ding Y.Q., Sun Q., Xu W. Real-Space Evidence of Rare Guanine Tautomer Induced by Water. ACS Nano. 2016;10:3776–3782. doi: 10.1021/acsnano.6b00393. PubMed DOI
Andersen E.S., Dong M.D., Nielsen M.M., Jahn K., Lind-Thomsen A., Mamdouh W., Gothelf K.V., Besenbacher F., Kjems J. DNA origami design of dolphin-shaped structures with flexible tails. ACS Nano. 2008;2:1213–1218. doi: 10.1021/nn800215j. PubMed DOI
Xu W., Kelly R.E.A., Gersen H., Laegsgaard E., Stensgaard I., Kantorovich L.N., Besenbacher F. Prochiral Guanine Adsorption on Au(111): An Entropy-Stabilized Intermixed Guanine-Quartet Chiral Structure. Small. 2009;5:1952–1956. doi: 10.1002/smll.200900315. PubMed DOI
Rothemund P.W.K. Folding DNA to create nanoscale shapes and patterns. Nature. 2006;440:297–302. doi: 10.1038/nature04586. PubMed DOI
Portalone G., Colapietro M. Redetermination of isocytosine. Acta Crystallogr. E. 2007;63:O1869–O1871. doi: 10.1107/S1600536807012494. DOI
Dračínský M., Jansa P., Ahonen K., Buděšínský M. Tautomerism and the Protonation/Deprotonation of Isocytosine in Liquid- and Solid-States Studied by NMR Spectroscopy and Theoretical Calculations. Eur. J. Org. Chem. 2011;2011:1544–1551. doi: 10.1002/ejoc.201001534. DOI
Dračínský M., Hodgkinson P. Solid-state NMR studies of nucleic acid components. RSC Adv. 2015;5:12300–12310. doi: 10.1039/C4RA14404J. DOI
Pohl R., Socha O., Šála M., Rejman D., Dračínský M. The Control of the Tautomeric Equilibrium of Isocytosine by Intermolecular Interactions. Eur. J. Org. Chem. 2018;2018:5128–5135. doi: 10.1002/ejoc.201800506. DOI
Pohl R., Socha O., Slavíček P., Šála M., Hodgkinson P., Dračínský M. Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations. Faraday Discuss. 2018;212:331–344. doi: 10.1039/C8FD00070K. PubMed DOI
Dračínský M., Jansa P., Chocholoušová J., Vacek J., Kovačková S., Holý A. Mechanism of the Isotopic Exchange Reaction of the 5-H Hydrogen of Uracil Derivatives in Water and Nonprotic Solvents. Eur. J. Org. Chem. 2011;2011:777–785. doi: 10.1002/ejoc.201001335. DOI
Štoček J.R., Bártová K., Čechová L., Šála M., Socha O., Janeba Z., Dračínský M. Determination of nucleobase-pairing free energies from rotamer equilibria of 2-(methylamino)pyrimidines. Chem. Commun. 2019;55:11075–11078. doi: 10.1039/C9CC05513D. PubMed DOI
Becke A.D. Density-Functional Thermochemistry 3. The Role of Exact Exchange. J. Chem. Phys. 1993;98:5648–5652. doi: 10.1063/1.464913. DOI
Lee C.T., Yang W.T., Parr R.G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron-Density. Phys. Rev. B. 1988;37:785–789. doi: 10.1103/PhysRevB.37.785. PubMed DOI
Barone V., Cossi M. Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J. Phys. Chem. A. 1998;102:1995–2001. doi: 10.1021/jp9716997. DOI
Cossi M., Rega N., Scalmani G., Barone V. Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J. Comput. Chem. 2003;24:669–681. doi: 10.1002/jcc.10189. PubMed DOI
Grimme S., Antony J., Ehrlich S., Krieg H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010;132:154104. doi: 10.1063/1.3382344. PubMed DOI
Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Scalmani G., Barone V., Petersson G.A., Nakatsuji H., et al. Gaussian 16, Revision A.03. Gaussian, Inc.; Wallingford, CT, USA: 2016.
Gerhardt V., Tutughamiarso M., Bolte M. Pseudopolymorphs of 2,6-diaminopyrimidin-4-one and 2-amino-6-methylpyrimidin-4-one: One or two tautomers present in the same crystal. Acta Crystallogr C. 2011;67:O179–O187. doi: 10.1107/S0108270111013072. PubMed DOI