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

International Journal of Molecular Sciences

Oleg V. Shishkinab²  Marcus Elstnerbc¹  Thomas Frauenheimc³ 

[1] Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;Department of Alkali Halide Crystals, Institute for Single Crystals, National Academy of Science of Ukraine, 60 Lenina ave., Kharkiv 61072, Ukraine. Phone: + 38 (0572) 30 79 73, Fax: + 38 (0572) 32 10 82, E-mail:;Department of Theoretical Physics, University of Paderborn, D-33098 Paderborn, Germany

关键词: Stacking dimers;    adenine-thymine Watson–Crick base pair;    structure;    intermo-lecular interaction;   

DOI  :  10.3390/i4100537

来源: mdpi

【 摘 要 】

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 C-H…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.

【 授权许可】

Unknown   
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