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An ab initio molecular orbital study on the stacking interaction between nucleic acid bases: Dependence on the sequence and relation to the conformation
Author(s) -
Aida Misako,
Nagata Chikayoshi
Publication year - 1986
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.560290522
Subject(s) - stacking , ab initio , chemistry , guanine , cytosine , nucleic acid , computational chemistry , sequence (biology) , ab initio quantum chemistry methods , dna , interaction energy , molecular orbital , crystallography , chemical physics , nucleotide , molecule , organic chemistry , biochemistry , gene
Abstract The stacking interaction energies between nucleic acid bases in A DNA and B DNA are calculated by means of the ab initio molecular orbital method. The calculated values agree well with the experimental values of stacking enthalpy changes. The stacking interaction energy is shown to be highly sequence dependent, particularly when the sequence includes guanine or cytosine. The possibility is shown that the conformation of a DNA double helix fragment is determined by the constituent stacking interaction. Electrostatic energy is the cause of the sequence dependency of the stacking energy, while charge transfer and dispersion energies contribute to the overall stability.