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Nonadditive nature of nucleobases interactions in model d(GpG) dinucleotide steps
Author(s) -
Cysewski Piotr
Publication year - 2010
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.22435
Subject(s) - stacking , chemistry , tetramer , intermolecular force , nucleobase , hydrogen bond , computational chemistry , character (mathematics) , molecule , dna , mathematics , biochemistry , organic chemistry , enzyme , geometry
High nonadditive character of intermolecular interaction energy (IIE) has been found for many d(GpG) dinucleotide steps in B‐DNA conformations. Although three‐ and four‐body terms posses opposite signs in all cases, positive nonadditivity is observed. On the other hand, the pairwise additive simplification may still be applied because there is linear correlation between magnitude of additive and nonadditive terms of IIE. The application of the linear regression leads to a higher accuracy with values of standard deviation about 0.5 kcal/mol. The heterogeneity of intermolecular interactions in two subsequent GC pairs was identified as the main source of nonadditivity. The higher the difference between hydrogen bonding and interstrand stacking, the higher the absolute values of three‐ and four‐body terms. This trend is of linear character and may be used for both parametric correction and measure of nonadditivity in d(GpG) steps without necessity of energy calculations for the whole tetramer. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011