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Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations

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ŠPONER Jiří MLÁDEK Arnošt ŠPAČKOVÁ Naděžda CANG Xiaohui H. CHEATHAM Thomas E. GRIMME Stefan

Rok publikování 2013
Druh Článek v odborném periodiku
Časopis / Zdroj Journal of the American Chemical Society
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www http://pubs.acs.org/doi/abs/10.1021/ja402525c
Doi http://dx.doi.org/10.1021/ja402525c
Obor Fyzikální chemie a teoretická chemie
Klíčová slova DENSITY-FUNCTIONAL THEORY; MOLECULAR-DYNAMICS SIMULATIONS; SUGAR-PHOSPHATE BACKBONE; APPROXIMATE COULOMB POTENTIALS; HUMAN TELOMERIC QUADRUPLEXES; ZETA VALENCE QUALITY; AUXILIARY BASIS-SETS; AMBER FORCE-FIELD; NUCLEIC-ACIDS; CRYSTAL-STRUCTURE
Popis We provide theoretical predictions of the intrinsic stability of different arrangements of guanine quadruplex (G-DNA) stems. Most computational studies of nucleic acids have applied Molecular Mechanics (MM) approaches using simple pairwise-additive force fields. The principle limitation of such calculations is the highly approximate nature of the force fields. In this study, we for the first time apply accurate QM computations (DFT-D3 with large atomic orbital basis sets) to essentially complete DNA building blocks, seven different folds of the cation stabilized two quartet G-DNA stem, each having more than 250 atoms. The solvent effects are approximated by COSMO continuum solvent We reveal sizable differences between MM and QM descriptions of relative energies of different G-DNA stems, which apparently reflect approximations of the DNA force field. Using the QM energy data, we propose correction to earlier free energy estimates of relative stabilities of different parallel, hybrid, and antiparallel G-stem folds based on classical simulations. The new energy ranking visibly improves the agreement between theory and experiment We predict the 5'-anti-anti-3' GpG dinucleotide step to be the most stable one, closely followed by the 5'-syn-anti-3' step. The results are in good agreement with known experimental structures of 2-, 3-, and 4-quartet G-DNA stems. Besides providing specific results for G-DNA, our study highlights basic limitations of force field modeling of nucleic acids. Although QM computations have their own limitations, mainly the lack of conformational sampling and the approximate description of the solvent, they can substantially improve the quality of calculations currently relying exclusively on force fields.
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