Biopolym. Cell. 2011; 27(3):221-230.
Molecular Biophysics
Intramolecular tautomerization and the conformational variability of some classical mutagens – cytosine derivatives: quantum chemical study
1, 2Brovarets' O. O., 1, 2Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Institute of High Technologies,
    Taras Shevchenko National University of Kyiv
    2, korp.5, Pr. Akademika Hlushkova, Kyiv, Ukraine, 03022


Aim. To determine the lifetime of the mutagenic cytosine derivatives through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atoms in molecules (AIM) theory and physicochemical kinetics were used. Results. It is shown that the modification of all investigated compounds, except DCyt, prevents their pairing in both mutagenic and canonical tautomeric forms with a base which is an interacting partner. This effect can inhibit their mutagenic potential. It is also established that Watson-Crick tautomeric hypothesis can be formally expanded for the investigated molecules so far as a lifetime of the mutagenic tautomers much more exceeds characteristic time for the incorporation of one nucleotides pair by DNA biosynthesis machinery. It seems that just within the frame of this hypothesis it will be possible to give an adequate explanation of the mechanisms of mutagenic action of N4-aminocytosine, N4-methoxycytosine, N4-hydroxycytosine and N4- dehydrocytosine, which have much more energy advantageous imino form in comparison with amino form. Conclusions. For the first time the comprehensive conformational analysis of a number of classical mutagens, namely cytosine derivatives, has been performed using the methods of non-empirical quantum chemistry at the MP2/6-311++G (2df,pd)//B3LYP/6-311++G(d,p) level of theory.
Keywords: point mutations of DNA, derivatives of cytosine, intramolecular tautomerization, Gibbs energy of activation, structural non-rigidity, analysis of the electron density topology


[1] Janion C. The efficiency and extent of mutagenic activity of some new mutagens of base-analogue type Mutat. Res 1978 56, N 3 P. 225–234.
[2] Janion C. Some problems of mutagenesis induced by base analogues Acta Biochim. Pol 1984 31, N 1 P. 183–192.
[3] Negishi K., Harada C., Ohara Y., Oohara K., Nitta N., Hayatsu H. N4-aminocytidine, a nucleoside analog that has an exceptionally high mutagenic activity Nucl. Acids Res 1983 11, N 15 P. 5223–5233.
[4] Nomura A., Negishi K., Hayatsu H., Kuroda Y. Mutagenicity of N4-aminocytidine and its derivatives in Chinese hamster lung V79 cells. Incorporation of N4-aminocytosine into cellular DNA Mutat. Res 1987 177, N 2 P. 283–287.
[5] Negishi K., Bessho T., Hayatsu H. Nucleoside and nucleobase analog mutagens Mutat. Res 1994 318, N 3 P. 227–238.
[6] Suzuki T., Moriyama K., Otsuka C., Loakes D., Negishi K. Template properties of mutagenic cytosine analogues in reverse transcription Nucl. Acids Res 2006 34, N 22 P. 6438– 6449.
[7] Reeves S. T., Beattie K. L. Base-pairing properties of N4-methoxydeoxycytidine 5'-triphosphate during DNA synthesis on natural templates, catalyzed by DNA polymerase I of Escherichia coli Biochemistry 1985 24, N 9 P. 2262–2268.
[8] Takahashi M., Nishizawa M., Negishi K., Hanaoka F., Yamada M. A., Hayatsu H. Induction of mutation in mouse FM3A cells by N4-aminocytidine-mediated replicational errors Mol. Cell. Biol 1988 8, N 1 P. 347–352.
[9] Hossain M. T., Chatake T., Hikima T., Tsunoda M., Sunami T., Ueno Y., Matsuda A., Takenaka A. Crystallographic studies on damaged DNAs: III. N4-methoxycytosine can form both Watson-Crick type and wobbled base pars in a B-form duplex J. Biochem 2001 130, N 1 P. 9–12.
[10] Moriyama K., Otsuka C., Loakes D., Negishi K. Highly efficient random mutagenesis in transcription-reverse-transcription cycles by a hydrogen bond ambivalent nucleoside 5'-triphosphate analogue: potential candidates for a selective anti-retroviral therapy Nucleosides, Nucleotides Nucleic Acids 2001 20, N 8 P. 1473–1483.
[11] Meervelt L. V., Lin P. K. T., Brown D. M. 6-(3,5-Di-O-acethyl-D-2-deoxyribofuranosyl)-3,4-dihydro-8H-pyrimi-do[4, 5-c] [1, 2]-oxazin-7(6H)-one Acta. Crystallogr., Sect. C 1995 51, N 7 P. 1347–1350.
[12] Popowska E., Janion C. The metabolism of N4-hydroxycytidine – a mutagen for Salmonella typhimurium Nucl. Acids Res 1975 2, N 7 P. 1143–1151.
[13] Negishi K., Takahashi M., Yamashita Y., Nishizawa M., Hayatsu H. Mutagenesis by N4-aminocytidine: induction of AT to GC transition and its molecular mechanism Biochemistry 1985 24, N 25 P. 7273–7278.
[14] Janion C., Glickman B. W. 4-hydroxycytidine: a mutagen specific for AT to GC transitions Mutat. Res 1980 72, N 1 P. 43–47.
[15] Singer B., Spengler S. Ambiguity and transcriptional errors as a result of modification of exocyclic amino groups of cytidine, guanosine, and adenosine Biochemistry 1981 20, N 5 P. 1127– 1132.
[16] Takahashi M., Negishi K., Hayatsu H. Proofreading of a mutagenic nucleotide, N4-aminodeoxycytidylic acid, by Escherichia coli DNA polymerase I Biochem. Biophys. Res. Communs 1987 143, N 1 P. 104–109.
[17] Aida M., Negishi K., Hayatsu H., Maeda M. Ab initio molecular orbital study of the mispairing ability of a nucleotide base analogue, N4-aminocytosine Biochem. Biophys. Res. Communs 1988 153, N 2 P. 552–557.
[18] Les A., Adamowicz L., Rode W. Structure and conformation of N4-hydroxycytosine and N4-hydroxy-5-fluorocytosine. A theoretical ab initio study Biochim. Biophys. Acta 1993 1173, N 1 P. 39–48.
[19] Brown D., Hewlins M., Schell P. The tautomeric state of N(4)hydroxyand N(4)-amino-cytosine derivatives J. Chem. Soc. Perkin 1 1968 15 P. 1925–1929.
[20] Fazakerley G. V., Gdaniec Z., Sowers L. C. Base-pair induced shifts in the tautomeric equilibrium of a modified DNA base J. Mol. Biol 1993 230, N 1 P. 6–10.
[21] Singer B., Fraenkel-Conrat H., Abbott L. G., Spengler S. J. N4Methoxydeoxycytidine triphosphate is in the imino tautomeric form and substitutes for deoxythymidine triphosphate in primed poly d[A-T] synthesis with E. coli DNA polymerase I Nucl. Acids Res 1984 12, N 11 P. 4609–4619.
[22] Brovarets O. O., Hovorun D. M. How stable are the mutagenic tautomers of DNA bases? Biopolym. Cell 2010 26, N 1 P. 72–76.