Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

The Study of the Nucleic Acid Base-Stacking by Monte Carlo Method: Extended Cluster Approach

In the last two years we have seen publications in this Journal on nucleic acids based on density functional theory and correlated ab initio calculations which examined sugar-phosphate backbone, base stacking, hydrogen bonding, even ring expansion and metal interactions. (1-3). Here a Metropolis Monte Carlo method based on the extended cluster approach is used to investigate adenine-thymine (A/T), adenine-uracil (A/U) and guanine-cytosine (G/C) base associates in a cluster containing 400 and 800 water molecules. It is shown that during the simulation each Watson-Crick base pair is transformed into a more favorable stacked configuration.

The results obtained allow to observe the whole process of convergence for the first time (for more information, visit the Web site http://vd.bitp.kiev.ua).

Table: Energetic characteristics of the transformation of hydrogen-bonded base pairs to the stacked associates and of the base stacking reaction in water cluster containing 400 molecules (in kcal mol).






AT base pair > A/T stacked dimer





AU base pair > A/U stacked dimer





GC base pair > G/C stacked dimer





A + T > A/T stacked dimer





A + U > A/U stacked dimer





G + C > G/C stacked dimer





It follows from this Table that all stacked associates in the water cluster are energetically more preferable to the corresponding Watson-Crick base pairs. The changes in the interaction energies show that the water–base interaction (ΔUwb) is the determining factor in favoring the stacked species over the base pair in an aqueous cluster. This may be due to the smaller hydrophobic surface of the stacks. The study showed that stacked dimers hydrate better than the hydrogen-bonded associates. The formation of the A-T, A-U and G-C base pairs in the water clusters was found to be energetically unfavorable, primarily due to the destabilizing contribution of the base-water interactions. The data allow us to calculate the transformation energy (ΔUtot) and its various contributions for all the three stacked associates investigated in the water cluster. These results are given in the Table.

As can be seen, the formation of all stacked dimers was found to be favorable, with transformation energies ranging from -8.8 to -15.8 kcal/mol. The preference for the formation of these stacks results mainly from the favourable change in the water-water interaction (Uww) and partly from the base-base interaction (Ubb) during the base association reaction.

In contrast to the Watson-Crick base pairs, the formation of all stacked associates is highly favorable. The water energy change, associated with the structural rearrangement of the water molecules around the bases during their association, contributes most to the stabilization of the stacks. The stacked associates are significantly less stabilized by the base-base interaction in comparison with the H-bonded base pairs. Yet to a lesser extent this applies to the water-base interactions. Thus, the water–water interaction is one of the main factors promoting stacked dimer formation, and the data are a direct confirmation of the crucial role of the water-water interaction in base stacking reported earlier in Ref. (4-6).


  1. D. Vasilescu, M. Adrian–Scotto, A. Fadiel, A. Hamza, J Biomol Struct Dyn 27, 465-476 (2010).
  2. P. Sharma, S. Sharma, A. Mitra, and H. Singh, J Biomol Struct Dyn 27, 65-81 (2009).
  3. G. V. Palamarchuk, O. V. Shishkin, L. Gorb, and J. Leszczynski, J Biomol Struct Dyn 26, 653-661 (2009).
  4. V. I. Danilov, I. S. Tolokh, J. Biomol. Struct. Dyn, 2, 119-130 (1984).
  5. V. I. Danilov, T. van Mourik, Molecular Physics 106, 1487 – 1494 (2008).
  6. V. I. Danilov, V. V. Dailidonis, T. van Mourik, H. Fruchtl (in preparation).

Victor I. Danilov
Vladimir V. Dailidonis
Tanja van Mourik
Herbert A. Früchtl

Institute of Molecular Biology and Genetics
National Academy of Sciences of Ukraine
150 Zabolotnoho St.
Kyiv, Ukraine., 03680