Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals.
Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of thw 162 analyzed tetramers both three- and four-body contributions are negligible except for d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal mol(-1). This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.
Cysewski
Piotr
P
Department of Physical Chemistry, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950, Bydgoszcz, Poland. piotr.cysewski@cm.umk.pl
D003460:Crystallization; D004247:DNA / Q000737:chemistry*; D004583:Electrons; D006147:Guanine / Q000031:analogs & derivatives / Q000737:chemistry; D008958:Models, Molecular; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D010084:Oxidation-Reduction; D011687:Purines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides; D011687:Purines; D011743:Pyrimidines; C024829:8-hydroxyguanine; D006147:Guanine; D004247:DNA
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