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Int. J. Mol. Sci. 2003, 4(10), 537-547; doi:10.3390/i4100537
Article

Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

1,2,* , 2,3, 3 and 2
1 Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina ave., Kharkiv 61072, Ukraine 2 Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany 3 Department of Theoretical Physics, University of Paderborn, D-33098 Paderborn, Germany
* Author to whom correspondence should be addressed.
Received: 1 April 2003 / Accepted: 1 September 2003 / Published: 29 September 2003
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Abstract

The structure of two isomeric stacked dimers of Watson-Crick 9-methyladenine-1-methylthymine pairs was fully optimized using an approximate density functional theory (DFT) method augmented with an empirical dispersion interaction. The results of the calculations reveal that head-to-tail (AT-TA) and head-to-head (AT-AT) dimers possess a significantly different geometry. The structure of both complexes is stabilized by vertical CH…O and C-H…N hydrogen bonds with the participation of the hydrogen atoms of the methyl groups. The energy of hydrogen bonding and stacking interactions was additionally calculated using the MP2/6-31G*(0.25) method. Differences in the mutual arrangement of the base pairs in two isomeric dimers lead to significant changes of intra and interstrand stacking interaction energies.
Keywords: Stacking dimers; adenine-thymine Watson–Crick base pair; structure; intermolecular interaction Stacking dimers; adenine-thymine Watson–Crick base pair; structure; intermolecular interaction
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).
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Shishkin, O.V.; Elstner, M.; Frauenheim, T.; Suhai, S. Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs. Int. J. Mol. Sci. 2003, 4, 537-547.

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