Ukr.Biochem.J. 2013; Том 85, № 4, липень-серпень, c. 98-103

doi: http://dx.doi.org/10.15407/ubj85.04.098

За яких умов вотсон-криківська пара основ ДНК G•C набуває всіх чотирьох конфігурацій, характерних для вотсон-криківської пари основ ДНК A•T?

06.04.2016   Без категорії   No comments

О. О. Броварець

Інститут молекулярної біології і генетики НАН України, Київ;
Науково-навчальний центр «Державна ключова лабораторія молекулярної
і клітинної біології», Київ, Україна;
Інститут високих технологій Київського національного університету
імені Тараса Шевченка, Українa;
e-mail: brovarets@list.ru

На рівні теорії MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) вперше показано, що льовдінівська пара основ G*·C* L, утворена мутагенними таутомерами, може набувати, як і вотсон-криківська пара основ ДНК A·T, чотирьох біологічно важливих конфігурацій, а саме: вотсон-криківської, оберненої вотсон-криківської, гугстинівської і оберненої гугстинівської. Цей факт демонструє доволі неочікувану роль таутомеризації однієї із вотсон-криківських пар основ ДНК, зокрема подвійним перенесенням протону: саме таутомеризація G·C→G*·C* дозволяє подолати стеричні перепони для реалізації вищезгаданих конфігурацій. Обговорюються геометричні, електронно-топологічні та енергетичні характеристики Н-зв’язків, що стабілізують досліджені пари, а також енергетичні характеристики останніх.

Ключові слова: , , , ,

Посилання:

  1. Watson JD, Crick FHC. Genetical implications of the structure of deoxyribonucleic acid. Nature. 1953 May 30;171(4361):964-7. PubMed, CrossRef
  2. Mishchuk YaR, Potyagaylo AL, Hovorun DM. Structure and dynamics of 6-azacytidine by MNDO/H quantum-chemical method. J Mol Struct. 2000;552(1-3):283-289. CrossRef
  3. Brovarets’ OO, Yurenko YP, Dubey IY, Hovorun DM. Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study. J Biomol Struct Dyn. 2012;29(6):597-605. PubMed, CrossRef
  4. Brovarets’ OO, Hovorun DM.  Can tautomerization of the A·T Watson-Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis. J Biomol Struct Dyn. 2014;32(1):127-54. PubMed, CrossRef
  5. Brovarets’ OO, Hovorun DM. Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis. J Biomol Struct Dyn. 2013;31(8):913-36. PubMed, CrossRef
  6. Tchurikov NA, Chistyakova LG, Zavilgelsky GB, Manukhov IV, Chernov BK, Golova YB. Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J Biol Chem. 2000 Aug 25;275(34):26523-9. PubMed, CrossRef
  7. Ghosal G, Muniyappa K. Hoogsteen base-pairing revisited: resolving a role in normal biological processes and human diseases. Biochem Biophys Res Commun. 2006 Apr 28;343(1):1-7. Review. PubMed, CrossRef
  8. Seaman FC, Hurley L. Interstrand cross-linking by bizelesin produces a Watson-Crick to Hoogsteen base-pairing transition region in d(CGTAATTACG)2. Biochemistry. 1993 Nov 30;32(47):12577-85. PubMed, CrossRef
  9. Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C. A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Res. 2002 Dec 1;30(23):5244-52. PubMed, PubMedCentral, CrossRef
  10. Nikolova EN, Kim E, Wise AA, O’Brien PJ, Andricioaei I, Al-Hashimi HM. Transient Hoogsteen base pairs in canonical duplex DNA. Nature. 2011 Feb 24;470(7335):498-502.  PubMed, PubMedCentral, CrossRef
  11. Hoogsteen K The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallographica. 1963 Sep;16(9): 907-916. CrossRef
  12. Zagryadskaya EI, Doyon FR, Steinberg SV. Importance of the reverse Hoogsteen base pair 54-58 for tRNA function. Nucleic Acids Res. 2003 Jul 15;31(14):3946-53. PubMed, PubMedCentral, CrossRef
  13. Haschemeyer AE, Sobell HM. The crystal structure of an intermolecular nucleoside complex: adenosine and 5-bromouridine. Proc Natl Acad Sci USA. 1963 Nov;50(5):872-7. PubMed, PubMedCentral, CrossRef
  14.  Löwdin PO. Proton Tunneling in DNA and its Biological Implications. Rev Mod Phys. 1963 Jul;35(3):724-732. CrossRef
  15. Löwdin PO. Quantum Genetics and the Aperiodic Solid: Some Aspects on the Biological Problems of Heredity, Mutations, Aging, and Tumors in View of the Quantum Theory of the DNA Molecule. Adv Quant Chem. 1966;2:213-360. CrossRef
  16. Brovarets’ OO, Kolomiets’ IM, Hovorun DM. / In Tomofumi Tada (Ed.), Quantum chemistry – molecules for innovations. Rijeka: In Tech Open Access, 2012. P. 59-102. CrossRef
  17. Kondratyuk IV, Samijlenko SP, Kolomiets’ IM, Hovorun DM. Prototropic molecular–zwitterionic tautomerism of xanthine and hypoxanthine. J Mol  Struct. 2000;523(1-3):109-118. CrossRef
  18. Pelmenschikov A, Hovorun DM, Shishkin OV, Leszczynski J. A density functional theory study of vibrational coupling between ribose and base rings of nucleic acids with ribosyl guanosine as a model system. J Chem Phys. 2000;113(14):5986-5990. CrossRef
  19. Shishkin OV, Pelmenschikov A, Hovorun DM, Leszczynski J. Theoretical analysis of low-lying vibrational modes of free canonical 2-deoxyribonucleosides. Chem Phys. 2000 Oct;260(3):317-325. CrossRef
  20. Samijlenko SP, Krechkivska OM, Kosach DA, Hovorun D. M. Transitions to high tautomeric states can be induced in adenine by interactions with carboxylate and sodium ions: DFT calculation data. J Mol Struct. 2004 Dec;708(1-3):97-104.  CrossRef
  21. Platonov MO, Samijlenko SP, Sudakov OO, Kondratyuk IV, Hovorun DM. To what extent can methyl derivatives be regarded as stabilized tautomers of xanthine? Spectrochim Acta A Mol Biomol Spectrosc. 2005 Nov;62(1-3):112-4. PubMed, CrossRef
  22. Danilov VI, Anisimov VM, Kurita N, Hovorun D. MP2 and DFT studies of the DNA rare base pairs: The molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases. Chem Phys Lett. 2005 Sep;412(4-6):285-293. CrossRef
  23.  Danilov VI, van Mourik T, Kurita N, Wakabayashi H, Tsukamoto T, Hovorun DM. On the mechanism of the mutagenic action of 5­bromouracil: a DFT study of uracil and 5­bromouracil in a water cluster. J Phys Chem A. 2009 Mar 19;113(11):2233-5. PubMed, CrossRef
  24. Yurenko YP, Zhurakivsky RO, Samijlenko SP, Hovorun DM. Intramolecular CH···O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their Watson-Crick pairs. Quantum chemical and AIM analysis. J Biomol Struct Dyn. 2011 Aug;29(1):51-65. PubMed, CrossRef
  25.  Brovarets’ OO, Hovorun DM. How stable are the mutagenic tautomers of DNA bases? Biopolym Cell. 2010;26(1):72-76.  CrossRef
  26. Brovarets’ OO, Hovorun DM. Stability of mutagenic tautomers of uracil and its halogen derivatives: the results of quantum-mechanical investigation. Biopolym Cell. 2010;26(4):295-298.  CrossRef
  27. Brovarets’ OO, Zhurakivsky RO, Hovorun DM. Is there adequate ionization mechanism of the spontaneous transitions? Quantum-chemical investigation. Biopolym Cell. 2010;26(5):398-405. CrossRef
  28. Brovarets’ OO, Hovorun DM. Intramolecular tautomerization and the conformational variability of some classical mutagens – cytosine derivatives: quantum chemical study. Biopolym Cell. 2011;27(3):221-230. CrossRef
  29. Brovarets’ OO, Hovorun DM. IR Vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine+ with cytosine and thymine: Quantum-chemical study.  Opt Spectrosc. 2011 Nov;111(5):750-757. CrossRef
  30. Brovarets’ OO, Zhurakivsky RO, Hovorun DM. The physico-chemical “anatomy” of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives. J Mol Model. 2013 Oct;19(10):4119-37. PubMed, CrossRef
  31. Hovorun DM, Gorb L, Leszczynski J. From the nonplanarity of the amino group to the structural nonrigidity of the molecule: A post-Hartree-Fock ab initio study of 2-aminoimidazole.  Int J Quantum Chem. 1999;75(3):245-253. CrossRef
  32. Boys SF, Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors.  Mol Phys. 1970 Oct;19(4):553-566. CrossRef
  33. Frisch MJ, Trucks GW, Schlegel HB. et al. Gaussian 09 (Revision B.01). Wallingford CT: Gaussian Inc., 2010.
  34. Bader RWF. Atoms in molecules. A quantum theory. Oxford: Clarendon Press, 1990. 436p.
  35. Keith TA. AIMAll (Version 11.12.19). 2011. Retrieved from http://aim.tkgristmill.com.
  36. Iogansen AV. Direct proportionality of the hydrogen bonding energy and the intensification of the stretching ν(XH) vibration in infrared spectra. Spectrochim Acta Part A. 1999 Jul;55(7-8):1585-1612. CrossRef
  37. Espinosa E, Molins E, Lecomte C. Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities. Chem Phys Lett. 1998 Mar;285(3-4):170-173. CrossRef
  38. Saenger W. Principles of nucleic acid structure. New York: Springer, 1984. 556p. CrossRef
  39. Bondi A. Van der Waals Volumes and Radii. J Phys Chem. 1964 Mar;68(3):441-451. CrossRef
  40. Kaplan I. Intermolecular interactions: Physical picture, computational methods and model potentials. Chichester: John Wiley & Sons Ltd., 2006. 367p. CrossRef
Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License.