Unique tautomeric and recognition properties of thioketothymines?

The tautomeric and recognition properties of thymine, 2- and 4-thioketothymines have been studied by means of accurate ab initio methods combined with molecular dynamics simulations and free energy calculations. In contrast to previous suggestions in the literature, the replacement of carbonyl oxygens by sulfur atoms does not lead to dramatic changes in tautomeric properties of the pyrimidine derivatives neither in vacuum nor in aqueous solution. Moreover, the presence of thioketothymines induces only mild changes in DNA structure, stability and fidelity.

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.

The anionic sugar-phosphate backbone of nucleic acids substantially contributes to their structural flexibility. To model nucleic acid structure and dynamics correctly, the potentially sampled substates of the sugar-phosphate backbone must be properly described. However, because of the complexity of the electronic distribution in the nucleic acid backbone, its representation by classical force fields is very challenging.

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data.

Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.

Base-stacking energies in ten unique B-DNA base-pair steps and some other arrangements were evaluated by the second-order Møller-Plesset (MP2) method, complete basis set (CBS) extrapolation, and correction for triple (T) electron-correlation contributions. The CBS(T) calculations were compared with decade-old MP2/6-31G*(0.25) reference data and AMBER force field.