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DNA structure and dynamics: Potential of interactions between two complementary DNA bases
Author(s) -
Yakushevich L. V.
Publication year - 2011
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.22735
Subject(s) - guanine , thymine , morse potential , dna , hydrogen atom , cytosine , base pair , computational chemistry , chemistry , nucleic acid , nucleobase , ab initio , quantum , hydrogen bond , simple (philosophy) , atom (system on chip) , quantum mechanics , chemical physics , physics , molecule , nucleotide , computer science , biochemistry , philosophy , epistemology , group (periodic table) , gene , embedded system
Specific interaction between two complementary nucleic acid bases, in which adenine forms two hydrogen bonds with thymine and guanine forms three hydrogen bonds with cytosine, is of great interest because it stabilizes the double helical DNA structure and because it determines the dynamics of the base pair opening that in turn is considered as one of important elements of the process of the DNA–protein recognition. To obtain the form of the potential of the interaction, investigators use many different methods including the most accurate ab initio quantum‐chemical calculations, approximate method of atom–atom potential functions, approximate mathematical formulas like the Morse potential, or empirical potentials. In this article, we derive a new mathematical formula of the potential. The formula is well grounded and advantageously differs from others because of its simplicity and convenience in practice. To derive the formula, we use a simple mechanical analog of two complementary DNA bases that consists of two coupled pendulums oscillating in the horizontal plane. We illustrate the applications of the formula to study small amplitude oscillations of the DNA complementary bases. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011