Biopolym. Cell. 2005; 21(5):440-445.
Molecular Biophysics
Stacking self-association of cytosine and its manifestation in optical spectra
1Petrushko I. A., 1Sukhoviya M. I.
  1. Uzhhorod National University
    54, Voloshyna Str., Uzhhorod, Ukraine, 88000


Geometrical and optical characteristics of cytosine stacking complexes have been studied by means of multi-configurational method in the frame of semiempirical Hamiltonian AM1 with full geometry optimization. An analysis of the bond lengths, spatial angles, vibration frequencies and electronic spectra in cytosine monomer, dimer and tetramer shows the changes in all aforementioned physical characteristics upon the complexing. The calculation predicts a high-frequency shift of the NH2-group valence vibrations. Intensity distribution of the electronic spectra bands of different cytosine complexes strongly depends on the number of molecules in the complex. A biophysical significance of the received results is discussed.
Keywords: cytosine complexes, physical characteristics, theoretical study


[1] Krasnokutski SA, Ivanov AY, Izvekov V, Sheina GG, Blagoi YP. FTIR matrix isolation study of uridine, thymidine, ribose, and glucose. J Mol Struct. 1999;482-483:249–52.
[2] Maleev V, Semenov M, Kruglova E, Bolbukh T, Gasan A, Bereznyak E, et al. Spectroscopic and calorimetric study of DNA interaction with a new series of actinocin derivatives. J Mol Struct. 2003;645(2-3):145–58.
[3] Hovorun DM. How structural changeability of nitrogen bases affects macroscopic properties of their crystals. Biopolym Cell. 1998;14(5):419-27.
[4] Kruglova EB, Dovbeshko GI, Krut'ko NA, Poshuk EP, Karpenko NA, Alesina MYu, Krasnitskaya AA. Investigation of structural damage in DNA molecules of gamma-irradiated rats. Vestn HNU 440. Biofiz Vestn. 1999; (4): 92-5.
[5] Morozov YuV, Bazhulin YaYa Electronic structure, spectroscopy and reactivity of molecules. Nucleobases, vitamins B6 and their analogs. Ed. Vol'kenshten. M .: Nauka, 1989. 288 p.
[6] Hobza P, Sponer J. Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. Chem Rev. 1999;99(11):3247-76.
[7] Sivanesan D, Babu K, Gadre SR, Subramanian V, Ramasami T. Does a Stacked DNA Base Pair Hydrate Better than a Hydrogen-Bonded One?: An ab Initio Study. J Phys Chem A. 2000;104(46):10887–94.
[8] Nir E, Hunig I, Kleinermanns K, de Vries MS. The nucleobase cytosine and the cytosine dimer investigated by double resonance laser spectroscopy and ab initio calculations. Phys Chem Chem Phys. 2003;5(21):4780-5.
[9] Petrushko IA, Tsud NM, Sukhoviya MI. Infrared spectroscopy of the effect of ultraviolet on the films structure of the cytosine, guanine and their complex. Vestn HNU 637 Biofiz Vestn. 2004; Iss 1-2 (14):23-26.
[10] Vinogradov IP, Zemskikh VV, Dodonova N Ye. The absorption spectra of nucleic acid bases (110-300 nm) and their luminescence excited in the vacuum ultraviolet region. Optika i spektroskopiya. 1974; 36(3):596-9.
[11] Sukhovija MI, Slavik VN, Shafranyosh II, Shimon LL. Interaction of nucleic acid bases molecules with low-energy electrons. Biopolym Cell. 1991; 7(6):77-82.
[12] Novikov VV. [Electromagnetic bioengineering]. Biofizika. 1998;43(4):588-93.
[13] Danilov VI. [Effect of hydration on the tautomerism of nucleic acid bases: computer simulation Monte Carlo]. Vestn HNU 466. Biofiz Vestn. 1999;(5):11-20.