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Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs
Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina ave., Kharkiv 61072, Ukraine
Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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
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
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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.
Shishkin OV, Elstner M, Frauenheim T, Suhai S. Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs. International Journal of Molecular Sciences. 2003; 4(10):537-547.
Shishkin, Oleg V.; Elstner, Marcus; Frauenheim, Thomas; Suhai, Sándor. 2003. "Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs." Int. J. Mol. Sci. 4, no. 10: 537-547.