Computational analysis of the stabilization effects in successive U-Hg-U base pairs


Ladislav Benda1,2, Michal Straka1, Vladimír Sychrovský1


1 Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic

2 Faculty of Mathematics and Physics, Charles University Prague, Ke Karlovu 3, 121 16 Praha 2, Czech Republic



Metal-DNA interactions represent one of the key topics in nucleic acid research. The idea of mercury complexing with DNA bases appeared already in early 1960’s [1]. HgII was shown to possess a very high affinity towards nitrogen atoms of nucleic acid bases [2]. Recently, a very stable structural pattern with mercury stabilizing a T-T mismatch inside double-strand DNA oligonucleotide has been revealed by means of NMR spectroscopy [3-5]. Furthermore, mercury binding to successive T-T mismatches inside DNA was also reported [3-4]. Theoretical studies of T-HgII-T base-pair properties followed the original experimental work [6-7].

            The present study uses computational tools to question the stabilization effects in successive T-HgII-T base pairs. By applying the RI-MP2 ab initio method we analyzed the nature of the attractive interaction between two U-HgII-U units, where uracil base was introduced instead of thymine in order to reduce the computational costs. By decomposing the interaction energy we identified the role of mercury in stabilizing the successive U-HgII-U base pairs. Significant interaction energy contributions arised from the charge redistribution on uracil rings induced by mercury, mercury through-space interaction with uracil of the other U-HgII-U unit, and Hg-Hg metallophilic attraction.



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